IncNS immersed boundary method SPM

143a6411...143d3f79 - 129 commits from branch master
dadd8e1e - First working script for the SPM method
85c7e74a - Phi defined as an expansion list
7d5745a0 - Added all projection types and dimensions
918b5cc0 - Now u_p is defined in session file
666a703a - Phi is defined in the session file now
44654176 - Spinning cylinder session files
fc24f6de - Shape function may depend on time
2539f779 - Phi and u_p may be functions of time
7ce27eaa - Example session files updated
45db5614 - New format for time-dependent functions
a6a8935d - New summary entry
0cb25335 - Updated example files
8b23d926 - Modification to VCS example file
0f0c538a - p_p BCs update only when Neumann
cbac90c8 - m_phi and m_up eval. at next time step
6a644ad4 - Added m_upPrev to store u_p^(n-1)
2aa823a7 - First approach to a force estimation function
c70bf460 - Still not working Forces module
97e7480b - Possible new grad(p_p) term to force IB vel. conds
f747b69a - New mesh for the IBM and VCS example cases
4ce1a451 - Testing of aero-forces integration
c4977249 - First working aero-force calculation implemented
79f0fdc6 - Time-history of aero-forces stored in std::vector
b142e36d - Output of EstimateForces to screen only if requested
d2e6e289 - Example file cyl_IBM.vcs uses FluidForces function
81a6b4fc - Redefined bad defined BCs in example files
5cf3cc0b - Aero forces are saved in a file, only for testing
0815e158 - Pressure cofficients update after final addition
fc20c7a4 - Removed vector storing aero-forces
46e32605 - Added AeroForcesSPM filter
067960fc - Static IBs can be read from STL files
ba1df239 - Scaling coeff as a parameter periodic BCs in p_p
da99f638 - Flow through wall correction as an option
c50f0d86 - New section for the SPM method on the developer guide.
01667161 - Updated example files and some format changes
1a81e0ab - Fixed correction pressure solver
c43a6680 - STL defined Phi is computed by FieldConvert now
edaafa5d - Fixes to FieldConvert phifile module
479d0a2d - Algorithm changed to use random directions
f96e3b72 - FieldConvert outputs Phi defined in session file
fcd237fb - ProcessPhiFromFile properly reads STL files
d752e799 - Removed some debug code
3c73e7de - Removed unused variables
386c2c81 - IncNavierStokesSolver reads phi function from FLD
dc5c1e4f - Clean up FindShortestDist function
a0615323 - Double check for points inside a triangle
3590d9c7 - Unused variable warning disabled
eb7a04c5 - ForceBoundary option debugged
7b522ac5 - Code reformatting after rebase
63051041 - phifile works w/o args if phi from session file
a9e79d20 - Added doc for the phifile FieldConvert module
2beb138b - STL phi implementing an octree
45629531 - Margin added to octree bounds / depth check
b0ae30d8 - Added comparison functions
42caad2c - Added comments
ce79fac4 - Added support for IMEXOrder4
4ba4fd36 - Reformatted some lines of SPM code
95f983d8 - Removed debug comments
7d5cd1af - Solved issues with 2.5D cases
a32a24eb - Forcing term now as an expansion 'm_fs'
ce4b7f20 - 'uint' to 'unsigned int' in STL module
87b79e88 - Format changes in STL module files
19852bfa - Shorten filter search
69c89ad1 - Corrected errors in developer guide SPM section
1916888e - Added pdf image file for SPM section
6675f9f9 - Added tests for the SPM solver
aa35fa92 - Added test for time-dependent Phi
373f486e - Added support for Taylor-Hood elements
9e3458b9 - SPM test files modified
583bbe13 - Changed name of 2D SPM test
4dce7278 - Merge branch 'feature/IncNS_SPM' of gitlab.nektar.info:nektar/nektar into feature/IncNS_SPM

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marked as a Work In Progress

added 1 commit

c2520261 - Changed layout of phifile command in docs

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unmarked as a Work In Progress

added 1 commit

115297ea - Impose the solid body velocity when phi is created from a STL file

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added 510 commits

115297ea...43ce760c - 508 commits from branch master
d058b083 - Merge branch 'master' into feature/IncNS_SPM
d403c280 - Updated files to be consistent with the new version

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added 1 commit

2884d7f2 - Moved the SPM docs from the developer guide to the user guide

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added 1 commit

c8adc5c9 - Added documentation for the 'AeroForcesSPM' filter.

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added 1 commit

bd3217ea - Updated num_elements() to size() in AeroForcesSPM filter

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added 1 commit

fabed9d3 - Added documentation of the phifile FieldConvert module

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added 227 commits

fabed9d3...21dc3e13 - 226 commits from branch master
b33ec73b - Merge branch 'master' into feature/IncNS_SPM

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assigned to @a_cassinelli

added fieldconvert incns-solver typeenhancement labels

@a_mateo I have finally finished reviewing this merge request. Thank you for developing this feature, truly excellent I have to say. Also thank you for making sure the code was well-commented code, it will definitely make it easier to take this up again in the future!

I tried to be as thorough as I could which means I opened a lot of review comments (38), but several are just cosmetic changes so should hopefully not take too much time to sort through it. For quick changes, I included suggestions which should make it easy for you to include them if you agree with my comments. I would maybe ask you the favour to double check that the lines fit within the 80 char width? I saw it in a couple of files but did not put a comment in every instance.

Once you have had a chance to have a look at my comments, you can also add a line in .CHANGELOG to highlight that this merge request introduced this SPM feature and we can then proceed to merge.

@dmoxey for what concerns the octree implementation to read STL files, I tried following through as closely as I could but I am not very familiar with this. Do you think you will have time to have a quick look (it would be files ProcessPhiFromFile.cpp + Octree.cpp)? The feature is rather self-contained so I am not too worried anyway!