Moved plane contact related stuff to own separate package
`MortarContact2D.jl`, where the development continues.
The following changes to test files are done:
1) Problem name for plane mortar coupling is `Mortar2D` (was `Mortar`
before), and later on 3d coupling will be `Mortar`. So the dimension
of coupling operator is explicitly given in a problem name.
2) Before elements to coupling was defined using
```julia
update!(problem.elements, "master elements", master_elements)
add_elements!(problem, [slave_elements; master_elements])
```
Now, explicitly give master and slave elements as
```julia
add_slave_elements!(problem, slave_elements)
add_master_elements!(problem, master_elements)
```
Keep on mind that Lagrange multipliers are in slave side.
A lot of code is moved to FEMBasis.jl regarding
calculating basis / shape functions of finite elements.
* add FEMBasis to REQUIRE
* remove obsolete files
* remove obsolete test files
* make integration point iterable
* loosen type definitions
* get length of element rather from basis than connectivity
* calculate midpoint of reference element
* wrong input argument to eval_basis! fixed
* refactored code for solvers.
* Added elementary tests for least-squares fitting of strain and stress fields
* A more realistic postprocess + Xdmf writing test
* removed debug keyword argument from test
* Rewrite update_xdmf!
New function to update Xdmf file no longer takes Solver object but
xdmf, problem, time and fields to write, for example
julia> update_xdmf!(xdmf, problem, 0.0, ["displacement", "temperature"])
All problems are written separately and put together into one
SpatialCollection, allowing to have more structured Xdmf and making
it easier to write complicated field configurations. Support for Xdmf
API 3.0 added.
* Support for Tensor6 field writing
* moved update_xdmf! to io.jl
* Removed some empty files
* Not use old Postprocessor, obsolete code.
* Not use old XDMF (obsolete code). Fixed test.
* removed some postprocessing to pass test, maybe we should drop abaqus.jl from code as obsolete
* add function get_temporal_collection back, it's used by update_xdmf of modal solver
* postprocess of boundary problems also
* added test for contact pressure. dl+quad test output was written in wrong file, fixed.
* postprocess for contact pressure
* contact pressure postprocess
* with boundary problems always store also the primary unknown field
* Change "reaction force" -> "lambda"
* testing postprocess of reaction force also
* sign convention
* new mortar segmentation tests which are failing
* test_problems_mortar_3d.jl: first test (Tet4) pass
* solvers.jl: diagonal of A is now properly filled, if that option is used. Another option is to remove zero rows from matrix system, which is on by default
* problems_mortar.jl: added new function diagnose_interface to calculate quantities from interface hopefully revealing bugs in calculation
* problems_mortar_3d.jl: added docstring for check_orientation! and removed flooding debug messages not helping to debug anything
* solvers.jl: Another way to solve Ax = b
* Refactored code to make implementation of Tri6 assemble! easier
* Patch test with linear Tet4 elements and quadratic Tet10 elements pass
When using quadratic elements, in polygon clipping algorithm element is divided to linear sub-elements as proposed in [Puso2008]. Interpolation of Lagrange multiplier space is done using quadratic shape functions.
References
----------
[Puso2008] Puso, Michael A., T. A. Laursen, and Jerome Solberg. "A segment-to-segment mortar contact method for quadratic elements and large deformations." Computer Methods in Applied Mechanics and Engineering 197.6 (2008): 555-566.
* increased coverage by adding diagnose_interface
* test using dual basis, failing for unknown reason
* Fixed dual basis construction for Mortar/Tet4
The coefficient matrix Ae for one particular slave element e is the result performing numerical integration on *all* integration cells associated with this element [Popp2013]. Ae cannot be calculated "cell-wise" like it was done before. Now patch test will pass also using `interface.properties.dual_basis = true` option. Partially integrated slave elements are supported as well.
References
----------
[Popp2013] Popp, Alexander, et al. "Improved robustness and consistency of 3D contact algorithms based on a dual mortar approach." Computer Methods in Applied Mechanics and Engineering 264 (2013): 67-80.
* Minor modifications to preprocess.jl
- removed two functions which are unimplemented (but maybe planned in future)
- added function create_node_set_from_element_set!, which can be used, like name suggests, to create a node set from nodes belonging to some set of elements.
* solvers.jl: now prints a list of overconstrained nodes which can be easily copy-pasted to problem.assembly.removed_dofs list to solver overconstrained situation manually
* Increase code coverage
Added a new test which tests dual basis 3d mortar + adjust option when using Tet4 in elasticity problem.
* Tet10 + Dual basis still failing, others are working
* mortar 3d low level tests
* linear surface element projection tests pass
* Introduced basis transform constant alpha
Tet10 + dual basis patch test still failing, but single element low level routine tests gives expected results with alpha=0.2
* added new integration rule FPG12 for triangular elements
* added drop_tolerance option to remove very small values from constraint matrices
* Introduced a basis transform matrix T
Constructing bi-orthogonal basis for quadratic surfaces is ill-conditioned. By doing a basis transform N' = N*T for slave side displacement vector it's possible to construct a bi-orthogonal basis in a same way than with linear elements. Setting alpha=0.2 ensures that quadratic basis functions are strictly positive in practical cases.
* fix 3d clipping test routine, accepts only 3d vertices
* dropped number of integration poitns from 12 to 7 in quadratic mortar surfaces intrestingly gives more accurate results, maybe something numerical error in FPG12 integration rule..?
* added two displacement patch tests + output writing for all cases
* %s/Int64/Int/g
* Changed test data location
* Fine tuning of logging levels
Jukka Aho