Cleanup of obsolete files

A lot of old files from old documentation systems etc. is in package.
These are now removed or moved. Old notebooks are in docs/tutorials.
This PR closes issue #124.
This commit is contained in:
Jukka Aho
2017-08-05 11:44:31 +03:00
parent 3d3e9bb441
commit 0f0c49da62
47 changed files with 1723 additions and 1163 deletions
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# JuliaFEM.abaqus_reader
## Internal
---
<a id="method__add_handler.1" class="lexicon_definition"></a>
#### add_handler(section, function_name) [¶](#method__add_handler.1)
Register new handler for parser
*source:*
[JuliaFEM/src/abaqus_reader.jl:18](https://github.com/JuliaFEM/JuliaFEM.jl/tree/b8194d0c137963b44aab6b223a22491f9b0f7774/src/abaqus_reader.jl#L18)
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# JuliaFEM.elasticity_solver
## Internal
---
<a id="method__assemble.1" class="lexicon_definition"></a>
#### assemble!(fe, eldofs_, I, V) [¶](#method__assemble.1)
Assemble global RHS to I,V ready for sparse format
Parameters
----------
fe : local vector
eldofs_ : Array
degrees of freedom
I,V : Arrays for sparse matrix
Notes
-----
eldofs can also be node ids for convenience. In that case dimension
is calculated and eldofs are "extended" to problem dimension.
*source:*
[JuliaFEM/src/elasticity_solver.jl:174](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L174)
---
<a id="method__assemble.2" class="lexicon_definition"></a>
#### assemble!(ke, eldofs_, I, J, V) [¶](#method__assemble.2)
Assemble global stiffness matrix to I,J,V ready for sparse format
Parameters
----------
ke : local matrix
eldofs_ : Array
degrees of freedom
I,J,V : Arrays for sparse matrix
Notes
-----
eldofs can also be node ids for convenience. In that case dimension
is calculated and eldofs are "extended" to problem dimension.
*source:*
[JuliaFEM/src/elasticity_solver.jl:133](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L133)
---
<a id="method__calc_local_matrices.1" class="lexicon_definition"></a>
#### calc_local_matrices!(X, u, R, K, basis, dbasis, lambda_, mu_, ipoints, iweights) [¶](#method__calc_local_matrices.1)
Calculate local tangent stiffness matrix and residual force vector
R = T - F for elasticity problem.
Parameters
----------
X : Element coordinates
u : Displacement field
R : Residual force vector
K : Tangent stiffness matrix
basis : Basis functions
dbasis : Derivative of basis functions
lambda : Material parameter
mu : Material parameter
ipoints : integration points
iweights : integration weights
Returns
-------
None
Notes
-----
If material parameters are given in list, they are interpolated to gauss
points using shape functions.
*source:*
[JuliaFEM/src/elasticity_solver.jl:76](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L76)
---
<a id="method__dummy.1" class="lexicon_definition"></a>
#### dummy(a) [¶](#method__dummy.1)
This is dummy function. Testing doctests and documentation.
Parameters
----------
x : Array{Float64, 1}
Returns
-------
Array{float64, 1}
x + 1
Notes
-----
This is dummy function
Raises
------
Exception
if things are not going right
Examples
--------
>>> a = [1.0, 2.0, 3.0]
>>> dummy(a)
[2.0, 3.0, 4.0]
*source:*
[JuliaFEM/src/elasticity_solver.jl:44](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L44)
---
<a id="method__eliminate_boundary_conditions.1" class="lexicon_definition"></a>
#### eliminate_boundary_conditions(dirichletbc, I, J, V) [¶](#method__eliminate_boundary_conditions.1)
Eliminate Dirichlet boundary conditions from matrix
Parameters
----------
dirichletbc : array [dim x nnodes]
I, J, V : sparse matrix arrays
Returns
-------
I, J, V : boundary conditions removed
Notes
-----
pros:
- matrix assembly remains positive definite
cons:
- maybe inefficient because of extra sparse matrix operations. (It's hard to remove stuff from sparse matrix.)
- if u != 0 in dirichlet boundary requires extra care
Raises
------
Exception, if displacement boundary conditions given, i.e.
DX=2 for some node, for example.
*source:*
[JuliaFEM/src/elasticity_solver.jl:221](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L221)
---
<a id="method__eliminate_boundary_conditions.2" class="lexicon_definition"></a>
#### eliminate_boundary_conditions(dirichletbc, I, V) [¶](#method__eliminate_boundary_conditions.2)
Eliminate Dirichlet boundary conditions from vector
Parameters
----------
dirichletbc : array [dim x nnodes]
I, V : sparse vector arrays
Returns
-------
I, V : boundary conditions removed
Notes
-----
pros:
- matrix assembly remains positive definite
cons:
- maybe inefficient because of extra sparse matrix operations. (It's hard to remove stuff from sparse matrix.)
- if u != 0 in dirichlet boundary requires extra care
Raises
------
Exception, if displacement boundary conditions given, i.e.
DX=2 for some node, for example.
*source:*
[JuliaFEM/src/elasticity_solver.jl:260](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L260)
---
<a id="method__solve_elasticity_increment.1" class="lexicon_definition"></a>
#### solve_elasticity_increment!(X, u, du, elmap, nodalloads, dirichletbc, lambda, mu, N, dNdchi, ipoints, iweights) [¶](#method__solve_elasticity_increment.1)
Solve one increment of elasticity problem
*source:*
[JuliaFEM/src/elasticity_solver.jl:281](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elasticity_solver.jl#L281)
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JuliaFEM.elasticity_solver
==========================
Internal
--------
.. function:: assemble!(fe, eldofs_, I, V)
Assemble global RHS to I,V ready for sparse format
:param fe : local vector
:param eldofs_ : Array
:param I,V : Arrays for sparse matrix
:notes: eldofs can also be node ids for convenience. In that case dimension
is calculated and eldofs are "extended" to problem dimension.
**source**
[JuliaFEM/src/elasticity_solver.jl:174]
.. function:: assemble!(ke, eldofs_, I, J, V)
Assemble global stiffness matrix to I,J,V ready for sparse format
:param ke : local matrix
:param eldofs_ : Array
:param I,J,V : Arrays for sparse matrix
:notes: eldofs can also be node ids for convenience. In that case dimension
is calculated and eldofs are "extended" to problem dimension.
**source**
[JuliaFEM/src/elasticity_solver.jl:133]
.. function:: calc_local_matrices!(X, u, R, K, basis, dbasis, lambda_, mu_, ipoints, iweights)
Calculate local tangent stiffness matrix and residual force vector
R = T - F for elasticity problem.
:param X : Element coordinates
:param u : Displacement field
:param R : Residual force vector
:param K : Tangent stiffness matrix
:param basis : Basis functions
:param dbasis : Derivative of basis functions
:param lambda : Material parameter
:param mu : Material parameter
:param ipoints : integration points
:param iweights : integration weights
:returns: None
:notes: If material parameters are given in list, they are interpolated to gauss
points using shape functions.
**source**
[JuliaFEM/src/elasticity_solver.jl:76]
.. function:: dummy(a)
This is dummy function. Testing doctests and documentation.
:param x : Array{Float64, 1}
:returns: Array{float64, 1}
x + 1
:notes: This is dummy function
:raises: Exception
if things are not going right
**source**
[JuliaFEM/src/elasticity_solver.jl:44]
.. function:: eliminate_boundary_conditions(dirichletbc, I, J, V)
Eliminate Dirichlet boundary conditions from matrix
:param dirichletbc : array [dim x nnodes]
:param I, J, V : sparse matrix arrays
:returns: I, J, V : boundary conditions removed
:notes: pros:
- matrix assembly remains positive definite
cons:
- maybe inefficient because of extra sparse matrix operations. (It's hard to remove stuff from sparse matrix.)
- if u != 0 in dirichlet boundary requires extra care
:raises: Exception, if displacement boundary conditions given, i.e.
DX=2 for some node, for example.
**source**
[JuliaFEM/src/elasticity_solver.jl:221]
.. function:: eliminate_boundary_conditions(dirichletbc, I, V)
Eliminate Dirichlet boundary conditions from vector
:param dirichletbc : array [dim x nnodes]
:param I, V : sparse vector arrays
:returns: I, V : boundary conditions removed
:notes: pros:
- matrix assembly remains positive definite
cons:
- maybe inefficient because of extra sparse matrix operations. (It's hard to remove stuff from sparse matrix.)
- if u != 0 in dirichlet boundary requires extra care
:raises: Exception, if displacement boundary conditions given, i.e.
DX=2 for some node, for example.
**source**
[JuliaFEM/src/elasticity_solver.jl:260]
.. function:: solve_elasticity_increment!(X, u, du, elmap, nodalloads, dirichletbc, lambda, mu, N, dNdchi, ipoints, iweights)
**source**
[JuliaFEM/src/elasticity_solver.jl:281]
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# JuliaFEM.interfaces
## Exported
---
<a id="method__solve_elasticity_interface.1" class="lexicon_definition"></a>
#### solve_elasticity_interface!() [¶](#method__solve_elasticity_interface.1)
This is generic interface that reads data from data model, solves elasticity
problem and updates model.
Parameters
----------
model : to be defined
*source:*
[JuliaFEM/src/interfaces.jl:22](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/interfaces.jl#L22)
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JuliaFEM.interfaces
===================
Exported
--------
.. function:: solve_elasticity_interface!()
This is generic interface that reads data from data model, solves elasticity
problem and updates model.
:param model : to be defined
**source**
[JuliaFEM/src/interfaces.jl:22]
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# JuliaFEM
## Exported
---
<a id="method__get_coordinates.1" class="lexicon_definition"></a>
#### get_coordinates(el::JuliaFEM.Element) [¶](#method__get_coordinates.1)
Return coordinates of element in array of size dim x nnodes
*source:*
[JuliaFEM/src/elements.jl:29](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L29)
---
<a id="method__integrate.2" class="lexicon_definition"></a>
#### integrate(f::Function) [¶](#method__integrate.2)
This version returns a function which must be operated with element e
*source:*
[JuliaFEM/src/math.jl:163](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L163)
---
<a id="method__integrate.3" class="lexicon_definition"></a>
#### integrate(f::Function, el::JuliaFEM.Element) [¶](#method__integrate.3)
Integrate f over element using Gaussian quadrature rules.
Parameters
----------
el::Element
well defined element
f::Function
Function to integrate
*source:*
[JuliaFEM/src/math.jl:143](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L143)
---
<a id="method__interpolate.1" class="lexicon_definition"></a>
#### interpolate(field::Float64, basis::Function, ip::Array{Float64, 1}) [¶](#method__interpolate.1)
Interpolate field variable using basis functions f for point ip.
This function tries to be as general as possible and allows interpolating
lot of different fields.
Parameters
----------
field :: Array{Number, dim}
Field variable
basis :: Function
Basis functions
ip :: Array{Number, 1}
Point to interpolate
*source:*
[JuliaFEM/src/math.jl:26](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L26)
---
<a id="method__linearize.2" class="lexicon_definition"></a>
#### linearize(f::Function, el::JuliaFEM.Element, field::ASCIIString) [¶](#method__linearize.2)
Linearize function f w.r.t some given field, i.e. calculate dR/du
Parameters
----------
f::Function
(possibly) nonlinear function to linearize
field::ASCIIString
field variable
Returns
-------
Array{Float64, 2}
jacobian / "tangent stiffness matrix"
*source:*
[JuliaFEM/src/math.jl:85](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L85)
---
<a id="method__linearize.3" class="lexicon_definition"></a>
#### linearize(f::Function, field::ASCIIString) [¶](#method__linearize.3)
This version returns another function which can be then evaluated against field
*source:*
[JuliaFEM/src/math.jl:100](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L100)
---
<a id="method__set_coordinates.1" class="lexicon_definition"></a>
#### set_coordinates(el::JuliaFEM.Element, coordinates) [¶](#method__set_coordinates.1)
Set coordinates for element
*source:*
[JuliaFEM/src/elements.jl:36](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L36)
## Internal
---
<a id="method__add_handler.1" class="lexicon_definition"></a>
#### add_handler(section, function_name) [¶](#method__add_handler.1)
Register new handler for parser
*source:*
[JuliaFEM/src/abaqus_reader.jl:13](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/abaqus_reader.jl#L13)
---
<a id="method__create_lagrange_element.1" class="lexicon_definition"></a>
#### create_lagrange_element(element_name, X, P, dP) [¶](#method__create_lagrange_element.1)
Create new Lagrange element
FIXME: this is not working
LoadError: error compiling anonymous: type definition not allowed inside a local scope
It's the for loop which is causing problems. See
https://github.com/JuliaLang/julia/issues/10555
*source:*
[JuliaFEM/src/elements.jl:64](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L64)
---
<a id="method__get_dbasisdx.1" class="lexicon_definition"></a>
#### get_dbasisdX(el::JuliaFEM.Element, xi) [¶](#method__get_dbasisdx.1)
Evaluate partial derivatives of basis function w.r.t
material description X, i.e. dbasis/dX
*source:*
[JuliaFEM/src/elements.jl:20](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L20)
---
<a id="method__get_element_id.1" class="lexicon_definition"></a>
#### get_element_id(el::JuliaFEM.Element) [¶](#method__get_element_id.1)
Get element id
*source:*
[JuliaFEM/src/elements.jl:43](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L43)
---
<a id="method__get_jacobian.1" class="lexicon_definition"></a>
#### get_jacobian(el::JuliaFEM.Element, xi) [¶](#method__get_jacobian.1)
Get jacobian of element evaluated at point xi
*source:*
[JuliaFEM/src/elements.jl:9](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L9)
---
<a id="method__integrate.1" class="lexicon_definition"></a>
#### integrate!(f::Function, el::JuliaFEM.Element, target) [¶](#method__integrate.1)
This version saves results inplace to target, garbage collection free
*source:*
[JuliaFEM/src/math.jl:178](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L178)
---
<a id="method__linearize.1" class="lexicon_definition"></a>
#### linearize!(f::Function, el::JuliaFEM.Element, field::ASCIIString, target::ASCIIString) [¶](#method__linearize.1)
In-place version, no additional garbage collection.
*source:*
[JuliaFEM/src/math.jl:118](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/math.jl#L118)
---
<a id="method__xdmf_new_model.1" class="lexicon_definition"></a>
#### xdmf_new_model() [¶](#method__xdmf_new_model.1)
Build a new model for outout
Parameters
----------
Example
-------
>>> xdmf_new_model()
*source:*
[JuliaFEM/src/xdmf.jl:48](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/xdmf.jl#L48)
---
<a id="method__xdmf_new_model.2" class="lexicon_definition"></a>
#### xdmf_new_model(xdmf_version) [¶](#method__xdmf_new_model.2)
Build a new model for outout
Parameters
----------
Example
-------
>>> xdmf_new_model()
*source:*
[JuliaFEM/src/xdmf.jl:48](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/xdmf.jl#L48)
---
<a id="type__point1.1" class="lexicon_definition"></a>
#### JuliaFEM.Point1 [¶](#type__point1.1)
1 node point element
*source:*
[JuliaFEM/src/elements.jl:112](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L112)
---
<a id="type__quad4.1" class="lexicon_definition"></a>
#### JuliaFEM.Quad4 [¶](#type__quad4.1)
4 node bilinear quadrangle element
*source:*
[JuliaFEM/src/elements.jl:155](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L155)
---
<a id="type__seg2.1" class="lexicon_definition"></a>
#### JuliaFEM.Seg2 [¶](#type__seg2.1)
3 node quadratic line element
*source:*
[JuliaFEM/src/elements.jl:139](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L139)
---
<a id="type__tet10.1" class="lexicon_definition"></a>
#### JuliaFEM.Tet10 [¶](#type__tet10.1)
10 node quadratic tethahedron
*source:*
[JuliaFEM/src/elements.jl:195](https://github.com/JuliaFEM/JuliaFEM.jl/tree/33a7fe664e9808c57564b507f0b8d5dcb451365a/src/elements.jl#L195)
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JuliaFEM
========
Exported
--------
.. function:: get_coordinates(el::JuliaFEM.Element)
**source**
[JuliaFEM/src/elements.jl:29]
.. function:: integrate(f::Function)
**source**
[JuliaFEM/src/math.jl:163]
.. function:: integrate(f::Function, el::JuliaFEM.Element)
Integrate f over element using Gaussian quadrature rules.
:param el: Element
:param f: Function
**source**
[JuliaFEM/src/math.jl:143]
.. function:: interpolate(field::Float64, basis::Function, ip::Array{Float64, 1})
Interpolate field variable using basis functions f for point ip.
This function tries to be as general as possible and allows interpolating
lot of different fields.
:param field : Array{Number, dim}
:param basis : Function
:param ip : Array{Number, 1}
**source**
[JuliaFEM/src/math.jl:26]
.. function:: linearize(f::Function, el::JuliaFEM.Element, field::ASCIIString)
Linearize function f w.r.t some given field, i.e. calculate dR/du
:param f: Function
:param field: ASCIIString
:returns: Array{Float64, 2}
jacobian / "tangent stiffness matrix"
**source**
[JuliaFEM/src/math.jl:85]
.. function:: linearize(f::Function, field::ASCIIString)
**source**
[JuliaFEM/src/math.jl:100]
.. function:: set_coordinates(el::JuliaFEM.Element, coordinates)
**source**
[JuliaFEM/src/elements.jl:36]
Internal
--------
.. function:: add_handler(section, function_name)
**source**
[JuliaFEM/src/abaqus_reader.jl:13]
.. function:: create_lagrange_element(element_name, X, P, dP)
**source**
[JuliaFEM/src/elements.jl:64]
.. function:: get_dbasisdX(el::JuliaFEM.Element, xi)
**source**
[JuliaFEM/src/elements.jl:20]
.. function:: get_element_id(el::JuliaFEM.Element)
**source**
[JuliaFEM/src/elements.jl:43]
.. function:: get_jacobian(el::JuliaFEM.Element, xi)
**source**
[JuliaFEM/src/elements.jl:9]
.. function:: integrate!(f::Function, el::JuliaFEM.Element, target)
**source**
[JuliaFEM/src/math.jl:178]
.. function:: linearize!(f::Function, el::JuliaFEM.Element, field::ASCIIString, target::ASCIIString)
**source**
[JuliaFEM/src/math.jl:118]
.. function:: xdmf_new_model()
Build a new model for outout
**source**
[JuliaFEM/src/xdmf.jl:48]
.. function:: xdmf_new_model(xdmf_version)
Build a new model for outout
**source**
[JuliaFEM/src/xdmf.jl:48]
.. function:: JuliaFEM.Point1
**source**
[JuliaFEM/src/elements.jl:112]
.. function:: JuliaFEM.Quad4
**source**
[JuliaFEM/src/elements.jl:155]
.. function:: JuliaFEM.Seg2
**source**
[JuliaFEM/src/elements.jl:139]
.. function:: JuliaFEM.Tet10
**source**
[JuliaFEM/src/elements.jl:195]
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# JuliaFEM.xdmf
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JuliaFEM.xdmf
=============
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API Documentation
=================
Automatically generated api documentation
Contents:
.. toctree::
:maxdepth: 3
JuliaFEM
JuliaFEM.elasticity_solver
JuliaFEM.interfaces