Slicing is very expensive operation on sparse matrices. Avoid slicing
by calculating matrix product `K_red = C1*K*C1`, where C1 is diagonal
matrix. This should be much cheaper.
Now style is to assemble all same kind/dimension elements at same time
in one function call, so it's possible to allocate all necessary
matrices only one time.
This function can be used to create elements from node set defined
in mesh. Resulting elements are of type Poi1, that is, they don't
have any volume but it's still possible to add boundary conditions
to them which are then enforced in discrete sense.
Problem arises typically when boundary condition is created using
"nodal" elements of type Poi1, but forget to define geometry and
```solvers("geometry", 0.0)``` fails in Xdmf update function. Fixed.
Yet another loop, but this way we can preallocate matrices when
constructiong local matrices of elements with same dimensions (which is
the case in practice)
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
Source code related to read and parse ABAQUS .inp files is now living in
it's own repository `AbaqusReader.jl` and in this commit we cleanup the
same files from this repository.
- add AbaqusReader to .travis.yml because it's not registered package yet
- initialize Mesh from AbaqusReader.jl dict
- remove ABAQUS tests and files moved to AbaqusReader.jl
- remove references to old module Abaqus
- move ABAQUS code to preprocess.jl (what is left)
- close issue #122
- close issue #55
* running v0.6 conversion code proposed by @ovainola in #108.
* change travis so that build is done using 0.6
* documentation is build from 0.6
* fix most of deprecation warnings
* fix test to pass 0.6
- MED file actually supports multiple element sets or node sets for
single element/node. This is now implemented.
- Minor cleanup of code, etc..
- Fixes issue #111.
- Added TimerOutputs.jl to REQUIRE file
- JuliaFEM has now TimerOutput handle `to` and function `print_statistics()` to get summary of time and memory usage
- TimerOutputs is used in LinearSolver at the moment and tested in file `test_elasticity_2d_linear_with_surface_load.jl`
* 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
* contact 3d patch test, standard lagrange, small sliding, linear tet4 elements
* tet4 dual basis contact patch test pass
* contact 3d patch test, standard lagrange, small sliding, linear tet4 elements
* tet4 dual basis contact patch test pass
* Patch test for linear elements standard lagrange / dual lagrange pass now
* Patch test for quadratic contact surfaces for standard + dual basis pass
* refactoring
* renamed files
* Improvements to preprocess scripts
* convert several elements to node sets in one command
* possibility to find particular node from mesh filtered by node set
* 2d small sliding contact patch test, linear elements
* Added backward compatibility
* 2d contact algorithms pass patch tests
* test data for 2d contacts
* no common models in different tests. testing generalized alpha stabilization
* Preprocess tests
* moved tests from test_preprocess_aster_reader.jl to test_preprocess.jl
* generalized-alpha time integration, alpha=0.0 by default
* Improvements to logging
* JuliaFEM.jl: can set environment variable to one of logging levels: OFF, CRITICAL, ERROR, WARNING, INFO, DEBUG
* problems_contact_2d_autodiff.jl: do not loop over nodes if logging level != DEBUG
* 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
* problems_mortar_3d.jl: rename function contains to approx_in
See issue #85. `contains` is now renamed to `approx_in`. I also
switched argument order, so this function is now called in a same
way function `in()`. Usage example:
julia> P = Vector[[1.0, 1.0], [2.0, 2.0]]
2-element Array{Array{T,1},1}:
[1.0,1.0]
[2.0,2.0]
julia> q = [1.0, 1.0] + eps(Float64)
2-element Array{Float64,1}:
1.0
1.0
julia> in(q, P)
false
julia> approx_in(q, P)
true
Also added docstring and usage example.
* Removed `importall base` from code
Change the code coverage to green.
* removed duplicate code
* Removed unused code
* removed unmaintained code
* DCTI + DVTI refactored
* discrete fields refactored and tested
* fields are now tested quite well.
* Removed obsolete code not used anywhere
* Element descriptions to common dictionary
* size in global const dictionary also
* Added coverage to sparse tools and removed couple unused functions
* get nonzero rows from SparseMatrixCSC
* bugfix: extending element basis now working and tested
* Removed two unused functions from elements.jl
* removed useless function
* Useless conversion
* remove elasticity assembly using ForwardDiff because it's not used anywhere'
* Added basic testing for NURBS. Fixed bug in NSolid interpolation.
* removed unused functions
* Removed some debug stuff
* renamed file
* removed field assembly posthook, i think not good idea at all
* test for nnz(K) == 0 and automatic determination of dofs
* Testing that solver is throwing error if having problems with boundary assembly
* Removed some unused options. Refactoring.
* Moved solver non-related code to elements.jl
* Removed custom exception (no need)
* unneeded postprocess code
* More tests for NURBS elements.
* Removed unfinished .mail parser
* proper use of Logging package
* also read results
* renamed test file
* create_surface_elements accepts surface name in String now
* bugfix: remove zero rows from constraint matrix after manually removing dofs from some boundary assemblies.
* New test, displacement 3d patch test
* skip displacement field in surface element splitting if not defined
* test element splitting and linear surface elements, fails.
* Bugfix: Xdmf, not XDMF
* removed nonworking tests, requires bugfix
* abaqus_read_results is not working -> bug
- Remove some obsolete tests related to Field.
- Fixed a test checking is header information found from source files
(was using FactCheck and commented out).
- Add header information for all files (was missing from
materials_plasticity.jl)
Jukka Aho