Shock Tube + YZB Discontinuity Capturing (#851)

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the

Shock Tube + YZB Discontinuity Capturing (#851)

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Style fixes

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Fluids: SETERRQ1 -> SETERRQ to be compatible with PETSc 3.17

* Fluids - Update shock-tube with #881

* Small fix to mid_point definition and removed repeat entries for Shock Tube problem in README.md.

* Including test output.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Fluids: SETERRQ1 -> SETERRQ to be compatible with PETSc 3.17

* Fluids - Update shock-tube with #881

* Fluids - added test output file for shocktube

* Small fix to mid_point definition and removed repeat entries for Shock Tube problem in README.md.

* Including test output.

* Update doc/sphinx/source/references.bib

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

* Update examples/fluids/README.md

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

* Update examples/fluids/index.md

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

* Update examples/fluids/navierstokes.h

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

* Update examples/fluids/problems/shocktube.c

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

* Update examples/fluids/qfunctions/shocktube.h

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

* Removed unused IFunction

* Added shocktube variables to SetupContext in advection.h, advection2d.h, and densitycurrent.h

* Missed some merge conflicts that have now been cleared up.

* Added helper function for covariant element length along a given vector.

* Added SetupContext to shocktube.h

* Fix to regression test path

* remove variable transpose of the Jacobian

* Fix index swap in implicit SUPG

* examples/fluids shocktube: fix stab summation and transpose

* delete IFunction

* example/fluids- updates reference solution

Co-authored-by: Timothy Aiken <timothyaiken@Timothys-MacBook-Pro.local>
Co-authored-by: Timothy Aiken <timothyaiken@cu-biot-10-10.203.167.69.int.colorado.edu>
Co-authored-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Timothy Aiken <timothyaiken@cu-genvpn-tcom-10.180.164.177.int.colorado.edu>
Co-authored-by: AdelekeBankole <adeleke.bankole@colorado.edu>

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feat: Add blasius boundary layer and channel flow examples to examples/fluids (#942)

* examples/fluids: Upload current case for collaboration

* examples/fluids: Replace developing BL with duct

feat: Add blasius boundary layer and channel flow examples to examples/fluids (#942)

* examples/fluids: Upload current case for collaboration

* examples/fluids: Replace developing BL with duct

* examples/fluids: Allow density to "float" at inflow

* fix: Add u_normal

* examples/fluids: bug fix in density flux

* examples/fluids: implement "floating" pressure; prescribed u, T

* examples/fluids: fixing initialization

We need has_neumann=true to get the weak boundary integrals called. It
is initialized in problem->setup_ctx and used in SetupLibceed(). This is
a hack to always apply.

* examples/fluids: include kinetic energy in Blasius IC

* examples/fluids: Blasius quasi-2D (slip in z planes)

* feat: Add Exact_Channel function

* feat: Use Exact_Channel for IC and Inflow

* examples/fluids: Add channel example

* examples/fluids: Define mu in blasius.c, cleanup

* examples/fluid: Add Blasius solution calculator

* examples/fluids: Add blasius IC and BCs

* Convert to implicit TS

* examples/fluids: Update blasius.yaml

* Move to ChannelContext, refactor DC and newtonian

- Added a dedicated ChannelContext, which allows for user setting of
flow parameters and consistent sharing of parameters between
QFunctions (instead of hardcoding)
- Moved density current (DC) specific settings from newtonian.c
densitycurrent.c

* Make gravity into vector quantity

* Add in body force for channel

* examples/fluids: remove explicitly setting coordinate field

This is created automatically now by DMPlex and DMProjectCoordinates
breaks (localized) periodicity, resulting in a tangled mesh.

* examples/fluids: transpose flux Jacobian in SUPG stabilization

* examples/fluids: update docs commensurate with flux Jacobian transpose fix

* examples/fluids: work on docs for tau

* examples/fluids: Increase blasius Re, implement Xi to SUPG

- Increased the Uinf and mu by 4x for the blasius problem
- Implemented the calculation of Xi for the SUPG term in newtonian.h

* examples/fluids: Remove flux jacobian transpose

- Removed for both eulervortex.h and newtonian.h

* examples/fluids: Reset Newtonian unit scaling to neutral

- Note that this resets the scaling for the densitycurrent problem,
thus the examples (and possibly tests) will probably need to be
changed

* examples/fluids: fix PetscOptionsBegin for new PETSc

* feat: Add slanted domain top surface

* feat: Add graded mesh option for blasius

* fix: Correct inflow boundary condition handling

* feat: Move to blasius_context, add CLI options

* feat: Move Blasius to physical air properties

* fix: Blasius profile and mesh generation

- Add the correct float->int rounding
- Fix eta to a value after exceeding the table's bounds

fix: Add fix eta after exceeding table

* examples/fluids: Move to physical mu default, fix tests

* doc: Add minimum documentation for channel and blasius

* examples/fluids: Add primitive jacobian and tau

- Also add misc comments

* examples/fluids: propose alternative flux Jacobian via prim-to-conservative

* examples/fluids: Add PHASTA diagonal tau

* fix: Add back in timestep obtaining

* examples/fluids: Add analytic tractions to inflow and outflow

- This is a stop-gap until viscous flux can be computed properly on the
boundary from current solution.
- Tau constants in a state of flux still but this produced a decent v at
inflow and outflow, removing the steep dive caused by forcing
dv/dx=-du/dy from a zero traction of omission.

* examples/fluids: CLI options for diagonal c_tau's

* examples/fluids: Update dt via context labels

* feat: Add more blasius table points

* examples/fluids: Cleanup stab and adjust Ctau_E

* examples/fluids: Replace spatial tau with diagonal

* examples/fluids: Fix stab in Euler

- Initialize `stab` to zero, add sum over loop

* examples/fluids: Document diagonal tau formulation

* examples/fluids: Fix compiler warnings

* examples/fluids: check error codes and elide unused header

* examples/fluids: Correct blasius example CLI

- Also add mention of the `blasius.yaml` file

* examples/fluids: Add supg to default blasius.yaml

* examples/fluids: Use yaml for channel and blasius

- Instead of long CLI options
- Also cleaned up the yaml formatting
- Added Cartesian directions to the faceMarker names

* examples/fluids: Show example yamls in README

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Kenneth E. Jansen <Kenneth.Jansen@colorado.edu>

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Merge pull request #949 from CEED/jeremy/small-doc-fix

Small doc update

minor - doc update and consistency for qextra

Merge pull request #881 from CEED/leila/fluids-mesh

Fluids - Update mesh creating and remove problem-specific BCs

Fluids - update README

Merge pull request #885 from CEED/jeremy/min-petsc

PETSc - set minimum version for examples

petsc - set minimum version for examples

Merge pull request #865 from CEED/leila/fluid-stab

Fluids - Fix bug in Stabilization (SU/SUPG)

examples/fluid: set c_tau = 0.5

examples/fluids: tau as spatial criterion 2 of hughesetal2010

Testing traveling vortex with

$ build/fluids-navierstokes -problem euler_vortex -ts_adapt_monitor -lx 1000 -ly 1000 -lz 50 -dm_plex_box

examples/fluids: tau as spatial criterion 2 of hughesetal2010

Testing traveling vortex with

$ build/fluids-navierstokes -problem euler_vortex -ts_adapt_monitor -lx 1000 -ly 1000 -lz 50 -dm_plex_box_faces 20,20,1 -ts_adapt_safety 0.8 -implicit -snes_atol 1e-3 -ksp_atol 1e-4 -ksp_rtol 1e-3 -ts_type alpha -ts_dt 0.1 -ksp_type bcgs -pc_type lu -log_view -snes_monitor -ksp_monitor -snes_converged_reason -output_freq 1 -degree 1 -ts_max_time 5. -stab supg -snes_lag_jacobian 30 -snes_lag_jacobian_persists -snes_mf_operator

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Merge pull request #818 from CEED/leila/doc-fix

Examples - doc

examples/fluids: doc - include "running the mini-app"

EULER_VORTEX - removed debugging tests from the test suite

conv_test.sh: Drop the euler_test option and degree 3 as the results almost never ma

examples/fluids: doc - include "running the mini-app"

EULER_VORTEX - removed debugging tests from the test suite

conv_test.sh: Drop the euler_test option and degree 3 as the results almost never match with different PETSc configurations

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Merge pull request #773 from CEED/leila/some-fix

Fluids - small fix in the README file

examples/fluids/README.md: fixed the link (from #754)

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memor

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memory for context problem

* freed allocated memory

* WIP: fluids: split density current into new compilation unit
I have dropped last changes before this commit so there might be some
bugs

* Fixed bugs after dropping the commit containing unnecessary changes

* NS: dropped unused variable from User struct

* WIP: factored out DMAddBoundary() for density_current

* split advection and advection2d into separate compilation units as well

* fluids: added *.o to make clean

* removed bc from problemData

* style

* commented the error handlers and moved petsc options regarding the boundary conditions to each compilation unit

* call bc functions inside SetUpDM()

* Moved all bc related statements from SetUpDM() to each compilation unit

* examples/fluids/advection.h: style

* WIP: modified CeedQFunctionContexts

* FFR: By creating a struct for DC context, one of the last test crushed so I had to reverse it. This should be investigated later.

* style

* examples/navierstokes: Use heap memory for ctxSetup

* examples/fluids: WIP - reading arrays through cl options for DC is enabled by using double pointers but there is still a problem with unit conversions and also need to fix other structs

* style

* WIP: Trying to assign values to context data in each problem function

* bug: there is a problem in pointer to struct

* WIP: Everything seems to be working but it breaks and I haven't figured out the reason ...

* fixed typo

* comment out stuff that have been moved to densitycurrent.c

* WIP: The first two regression test pass. There is a problem with stabilization.

* style

* Fluids: QFContext -> Physics

* WIP: passing StabilizationType to Physics (but PETSc is not happy and it diverges for SU and SUPG)

* Initial commit for refactoring advection(2d)

* WIP: Advection is set up except for wind_type

* WIP: refactored advection2d; need to fix the BCs for translation and also passing implicit to advection correctly

* WIP: pass wind_type to all functions correctly but there is still a problem with BCs in the case of translation (changes are not applied to advection yet)

* Apply the same fixes for BCs in advection

* Fluids - Refactor: Moved warnings to advection(2d)

* Fluids - Refactor: remove dead code

* Fluids - Refactor: Move *.h to /qfunctions and *.c to /src

* style

* Fluids - Refactor: drop the supg regression test for now

We need to debug SU/SUPG for density_current. The test does not work.

* Fluids - Refactor: Fixed the double-pointer issue

* Fluids - Refactor: Assign ctxSetup->time = 0 inside each problem's *.c

* Fluids - Refactor: make implicit a member of Physics

* Fluids - Refactor: Add warning for the usage of explicit and supg

* Some comments and naming

* Merge main after v0.8 (#723)

* Fluids - Five regression tests added for euler_vortex

* Fluids - Drop some of the regression tests for now (Needs to get fixed)

* Fluids - Moved all functions to their corresponding source files

* Fluids - move problem source files to /problems

* Fluids - drop dead regression test reference files

* Fluids - more consistent file names

* Fluids - drop dead code and comments

* Fluids - removed CreateVectorFromPetscVec() since it was only used once

* Fluids - created AppCtx for cl option variables and moved cl options to a cloption.c

* Fluids: change style of AppCtx

* style

* Fluids: /src -> /utils

* Created CreateDistributedDM() and some style

* Fluids - create RegisterProblem()

* style - minor

* style - minor

* Fluids - some more C style

* Fluids - /utils -> /src

* Fluids - create VizRefineDM() for viz_refine

* Fluids: some style and name change

* Fluids - style

* Fluids - remove the second ceed initialization

* Fluids - Created CeedData and SetupLibCEED()

* Fluids - create SetupContextForProblems()

* Fluids - Assign structs after they are created

* Fluids - style, minor

* Fluids - created RegressionTests_NS

* Fluids - created GetError_NS()

* Fluids - created PrintOutput_NS()

This processes bash output except for the problem summary which will be
included after mem_type is managed properly.

* Fluids - remove unused variables

* Fluids - created TSSolve_NS() which creates, sets up, and solves ts

* Fluids: Fixed a bug caused by merging#714

* Fluids - style

* Fluids - created SetupICsFromBinary() for case of -continue

* Fluids - create SetBCsFromICs_NS()

* Fluids - default degree had is 1 not 2

* Fluids: clean-up

* Fluids: style - minor

* Fluids - drop redundant operation

* Fluids: clean-up SetupLibCEED()

* Fluids: style - minor

* Fluids: WIP - C style

* Fluids: style - minor

* Fluids: move ceed vector creation to SetupLibCEED()

* Fluids: WIP - clean-up CreateOperatorForDomain()

* Fluids: major clean-up in CreateOperatorForDomain()

* Fluids: style - minor

* Fluids: drop VectorPlacePetscVec()

* Fluids: move ICs_FixMultiplicity() to misc.c

* Fluids: WIP - C style

* Fluids: fix merge conflict after d63eecaab22a26d3072677a1b66c0cf77aa9009d

* Fluids: drop unused function call DMLocalizeCoordinates()

* Fluids: replace user requested memType with MemTypeP2C()

* Fluids: C style

* Fluids: Q->num_Q (Q (# qpts) and Q (global state vector) were confusing my fresh petsc config)

* Fluids: WIP - add GPU vectors

* Fluids: Fixed the memory leak caused by Physics struct

* Fluids: style -minor

* Fluids: no need for casting

* Fluids: Fix mem leak (q0_ceed had to be destroyed at the end of navierstokes.c)

* Fluids: Fixed all mem leaks

* Fluids: Set VecType for dm_hierarchy

* Fluids/doc: fix style

* Fluids: fix missing VecRestoreArray()

* Fluids: clean-up ComputeLumpedMassMatrix()

* Fluids: Cleanup ICs_FixMultiplicity()

* Fluids: WIP - cleanup setupts.c

* Fluids: style - minor

* Fluids: Create element coord ceed vector locally and drop it from CeedData

* Fluids: fix some todos

* Fluids: drop unused code for EULER BCs

* Fluids: PetscMalloc1 -> PetscCalloc1

* Fluids - Define BCs for ADVECTION(2D) for all cases without having the user specify them and change the regressions accordingly

ToDo: For some reason I can't create new regression tests for explicit scheme.

* Fluids - Define problem->print_info() for each problem

* Fluids: Shorten some problem specific command line variables & style

* Fluids - Cleanup BCs in the translation mode

* Fluids - cleanup

* Fluids - more cleanup in BCs

* Fluids - Updated doc, README, and cleanup in the code and cl options

* Fluids - add more regression tests

* Fluids - Define tolerance for the convergence test

* Fluids: include x_coord in CeedData

* wip - gpu

Revert "Fluids: include x_coord in CeedData"

I had to revert this commit since it crashes DC

* style

* Fluids - remove unused variables

* Fluids - fix unused function warnings

* Fluids - fix the remaining warnings

* Fluids - style

* Fluids - add missing licence

* Fluids - bring back contexts to the QFunction header files

* Fluids - transfer QFunctions for boundary integral to their corresponding setupgeo(2d).h header files and add description for Setup2d

* fluids - fix context data sizes

* GPU - add helper function macro

* ex - use consistent MPI info output

* GPU - improve CEED_QFUNCTION_HELPER macro, more flexible

* Fluids - turn on some gpu tests

* Fluids - bring back element coordinate to CeedData

* Fluids - cleanup

* qfunction - clean up helper function macro

* Fixed the remaining conflicts from #769 (helped-by: @rezgarshakeri)

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: jeremylt <thompson.jeremy.luke@gmail.com>

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Merge branch 'euler-vortex-test' (#601)

* euler-vortex-test: (126 commits)
examples/fluids/conv_plot.py: clean-up
examples/fluids: Some clean-up in the post-processing files
examples/fluids: E

Merge branch 'euler-vortex-test' (#601)

* euler-vortex-test: (126 commits)
examples/fluids/conv_plot.py: clean-up
examples/fluids: Some clean-up in the post-processing files
examples/fluids: ETV - the convergence test comparison was failing since P_inlet is now hard-coded for each test and doesn't go through the scaling
examples/fluids: ETV - a better conditional statement for incoming T and P
examples/fluids: ETV - removed old cl options
examples/fluids: ETV - drop stabilization
examples/fluids: ETV - more clean-up
examples/fluids: ETV - removed unused variables
examples/fluids: ETV - removed the support for the forcing terms required for mms
ETV: some clean-up
ETV: ke -> E_kinetic for consistency
examples/fluids: remove T_inlet and P_inlet cl options and hard code them for each case
examples/fluids: fix warning about the stab option usage
examples/fluids: fix broken advection(2d) problem
examples/fluids: removed vortex_strength from SetupContext
examples/fluids: remove unused context from SetUpDM()
examples/fluids: bring back missing VecView function call
examples/fluids: fix typo in comments
README: style
README: Added in/outflow BCs for ADVECTION
...

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README: style

README: Added in/outflow BCs for ADVECTION

README: Added Euler Traveling Vortex

Merge pull request #714 from CEED/leila/ex-output-dir

Fluids & Solids | add/modify cl options for viz output folder

Command line option for viz in Fluids and Solids examples

examples/fluids: change the cl option -of to -output_dir for the output folder

examples/solids: add cl option -output_dir for the viz outpu

Command line option for viz in Fluids and Solids examples

examples/fluids: change the cl option -of to -output_dir for the output folder

examples/solids: add cl option -output_dir for the viz output

change: output folder -> output directory

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

examples: change variable name outputfolder -> outputdir

examples: update the README files

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Merge branch 'main' into natalie/hip-ref-v2

Merge branch 'leila/bc' [PR #540]

* leila/bc: (57 commits)
examples/fluids: fix doc
examples/fluids: comments on ICs and BCs & style
NS: style
examples/fluids: CreateRestrictionFromPlex: han

Merge branch 'leila/bc' [PR #540]

* leila/bc: (57 commits)
examples/fluids: fix doc
examples/fluids: comments on ICs and BCs & style
NS: style
examples/fluids: CreateRestrictionFromPlex: handle empty domainIS
examples/fluids: style
examples/fluids/advection.h: spherical bubble is the default IC
examples/fluids: style
examples/fluids/advection.h: fixed in/outflow signs for implicit scheme
examples/fluids: comments
examples/fluids: PetscBool -> bool in QFunctions
examples/fluids: removed periodicity from the setup struct
examples/fluids: clear DS and fields in -viz_refine
examples/fluids/setup-boundary.h: comment
examples/fluids/advection2d.h: removed unused variables
doc/NS: update
examples/fluids/advection.h: spherical bubble is the default IC
examples/fluids: fix sign and simplify advection2d inflow/outflow for implicit/explicit
examples/fluids: u_* = u_R on inflow boundaries
doc: added representative runs for TRANSLATION mode
examples/fluids: Total Energy is now prescribed for inflow BCs and can be changed using -E_wind
...

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examples/fluids: Total Energy is now prescribed for inflow BCs and can be changed using -E_wind

initial commit for specifying total energy instead of pressure and density for inflow BCs

update navi

examples/fluids: Total Energy is now prescribed for inflow BCs and can be changed using -E_wind

initial commit for specifying total energy instead of pressure and density for inflow BCs

update navierstokes.c

update README

update doc

comments updated

prescribe E_wind = 1.e6

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