diff --git a/Makefile b/Makefile deleted file mode 100644 index c6f5a5f..0000000 --- a/Makefile +++ /dev/null @@ -1,246 +0,0 @@ - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = docs/build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) -endif - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -# ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) docs -ALLSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) docs -# the i18n builder cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext build apidoc copyreadme convert_notebooks wwwdeploy - - -#build: -# julia -e 'Pkg.init(); Pkg.clone(pwd()); Pkg.build("JuliaFEM")' - -#build: -# julia -e 'Pkg.init(); Pkg.clone(pwd(), "JuliaFEM"); Pkg.build("JuliaFEM")' - -build: - julia -e 'Pkg.build("JuliaFEM")' - -# create .md files from function docstrings -apidoc: - julia docs/build_api.jl - -# copy readme to correct place in docs root -#copyreadme: -# cp README.md docs/index.md - -# convert notebooks to md files -convert_notebooks: - julia docs/build_notebooks.jl - -fix_permissions: - find docs/build/html -type d -exec chmod 775 {} \; && find docs/build/html -type f -exec chmod 664 {} \; - -lint: - julia docs/build_lint.jl - -unittests: - julia docs/build_unittests.jl - -doctests: - julia docs/build_doctests.jl - -.PHONY: test - -test: - julia -e 'Pkg.test("JuliaFEM")' - -# usage: make test_file FILE=test/test_heat.jl -# or even: watch make test_file FILE=test/test_heat.jl -test_file: - timeout 30 julia -e 'using JuliaFEM.Test; run_test("$(FILE)"); print_test_statistics()' - -# usage: make test_function FILE=test/test_fields.jl FUNCTION=test_increment -# or even: watch ... -test_function: - julia -e 'using JuliaFEM.Test; run_test("$(FILE)", :$(FUNCTION)); print_test_statistics()' - -pillu: - julia -e 'println("\x1b[31m\"red\"\x1b[0m")' - -#coverage_report: -# julia -e 'Pkg.test("JuliaFEM"; coverage=true); cd(Pkg.dir("JuliaFEM")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())' - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " applehelp to make an Apple Help Book" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " texinfo to make Texinfo files" - @echo " info to make Texinfo files and run them through makeinfo" - @echo " gettext to make PO message catalogs" - @echo " changes to make an overview of all changed/added/deprecated items" - @echo " xml to make Docutils-native XML files" - @echo " pseudoxml to make pseudoxml-XML files for display purposes" - @echo " linkcheck to check all external links for integrity" - @echo " doctest to run all doctests embedded in the documentation (if enabled)" - @echo " coverage to run coverage check of the documentation (if enabled)" - -clean: - rm -rf $(BUILDDIR)/* - -html: - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html - @echo - @echo "Build finished. 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The XML files are in $(BUILDDIR)/xml." - -pseudoxml: - $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml - @echo - @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/contributors b/contributors deleted file mode 100644 index d3d09e6..0000000 --- a/contributors +++ /dev/null @@ -1,3 +0,0 @@ -Tero Frondelius -Jukka Aho -Olli Väinölä diff --git a/docs/_static/build-failing-red.svg b/docs/_static/build-failing-red.svg deleted file mode 100644 index 2c9f5e0..0000000 --- a/docs/_static/build-failing-red.svg +++ /dev/null @@ -1 +0,0 @@ -buildbuildfailingfailing \ No newline at end of file diff --git a/docs/_static/build-passing-brightgreen.svg b/docs/_static/build-passing-brightgreen.svg deleted file mode 100644 index e090578..0000000 --- a/docs/_static/build-passing-brightgreen.svg +++ /dev/null @@ -1 +0,0 @@ -buildbuildpassingpassing \ No newline at end of file diff --git a/docs/_static/build-unknown-lightgrey.svg b/docs/_static/build-unknown-lightgrey.svg deleted file mode 100644 index c72a2f5..0000000 --- a/docs/_static/build-unknown-lightgrey.svg +++ /dev/null @@ -1 +0,0 @@ -buildbuildunknownunknown \ No newline at end of file diff --git a/docs/api/JuliaFEM.abaqus_reader.md b/docs/api/JuliaFEM.abaqus_reader.md deleted file mode 100644 index dd7c3a0..0000000 --- a/docs/api/JuliaFEM.abaqus_reader.md +++ /dev/null @@ -1,14 +0,0 @@ -# JuliaFEM.abaqus_reader - -## Internal - ---- - - -#### 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) - diff --git a/docs/api/JuliaFEM.elasticity_solver.md b/docs/api/JuliaFEM.elasticity_solver.md deleted file mode 100644 index 826f317..0000000 --- a/docs/api/JuliaFEM.elasticity_solver.md +++ /dev/null @@ -1,190 +0,0 @@ -# JuliaFEM.elasticity_solver - -## Internal - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - diff --git a/docs/api/JuliaFEM.elasticity_solver.rst b/docs/api/JuliaFEM.elasticity_solver.rst deleted file mode 100644 index 557fa39..0000000 --- a/docs/api/JuliaFEM.elasticity_solver.rst +++ /dev/null @@ -1,103 +0,0 @@ -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] - diff --git a/docs/api/JuliaFEM.interfaces.md b/docs/api/JuliaFEM.interfaces.md deleted file mode 100644 index 85d78e7..0000000 --- a/docs/api/JuliaFEM.interfaces.md +++ /dev/null @@ -1,19 +0,0 @@ -# JuliaFEM.interfaces - -## Exported - ---- - - -#### 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) - diff --git a/docs/api/JuliaFEM.interfaces.rst b/docs/api/JuliaFEM.interfaces.rst deleted file mode 100644 index 5bb7a45..0000000 --- a/docs/api/JuliaFEM.interfaces.rst +++ /dev/null @@ -1,15 +0,0 @@ -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] - diff --git a/docs/api/JuliaFEM.md b/docs/api/JuliaFEM.md deleted file mode 100644 index 5fafb0c..0000000 --- a/docs/api/JuliaFEM.md +++ /dev/null @@ -1,260 +0,0 @@ -# JuliaFEM - -## Exported - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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 - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - ---- - - -#### 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) - diff --git a/docs/api/JuliaFEM.rst b/docs/api/JuliaFEM.rst deleted file mode 100644 index 97d884f..0000000 --- a/docs/api/JuliaFEM.rst +++ /dev/null @@ -1,130 +0,0 @@ -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] - diff --git a/docs/api/JuliaFEM.xdmf.md b/docs/api/JuliaFEM.xdmf.md deleted file mode 100644 index df1875a..0000000 --- a/docs/api/JuliaFEM.xdmf.md +++ /dev/null @@ -1,2 +0,0 @@ -# JuliaFEM.xdmf - diff --git a/docs/api/JuliaFEM.xdmf.rst b/docs/api/JuliaFEM.xdmf.rst deleted file mode 100644 index 79f91c8..0000000 --- a/docs/api/JuliaFEM.xdmf.rst +++ /dev/null @@ -1,3 +0,0 @@ -JuliaFEM.xdmf -============= - diff --git a/docs/api/index.rst b/docs/api/index.rst deleted file mode 100644 index 39a18e4..0000000 --- a/docs/api/index.rst +++ /dev/null @@ -1,14 +0,0 @@ -API Documentation -================= - -Automatically generated api documentation - - -Contents: - -.. toctree:: - :maxdepth: 3 - - JuliaFEM - JuliaFEM.elasticity_solver - JuliaFEM.interfaces diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index d75cba7..0000000 --- a/docs/conf.py +++ /dev/null @@ -1,315 +0,0 @@ -# -*- coding: utf-8 -*- -# -# JuliaFEM documentation build configuration file, created by -# sphinx-quickstart on Fri Jul 3 22:25:04 2015. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import sys -import os -import juliadoc -import shlex -import sphinx_rtd_theme -import datetime - -html_last_updated_fmt = "%Y-%m-%d %H:%M:%S" - -extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.doctest', - 'sphinx.ext.coverage', - 'sphinx.ext.viewcode', - 'juliadoc.julia', - 'juliadoc.jlhelp', - 'numpydoc'] - -html_theme_path = [ - juliadoc.get_theme_dir(), - sphinx_rtd_theme.get_html_theme_path()] - -html_sidebars = juliadoc.default_sidebars() - -primary_domain = 'jl' -highlight_language = 'julia' - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -#extensions = [] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# source_suffix = ['.rst', '.md'] -source_suffix = ['.rst', '.md'] - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'JuliaFEM' -copyright = u'2015, Jukka Aho, Olli Väinölä, Tero Frondelius' -author = u'Jukka Aho, Olli Väinölä, Tero Frondelius' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '0.0.1' -# The full version, including alpha/beta/rc tags. -release = '0.0.1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all -# documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -#add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] - -# If true, keep warnings as "system message" paragraphs in the built documents. -#keep_warnings = False - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# html_theme = 'alabaster' -html_theme = 'sphinx_rtd_theme' - - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -html_show_sphinx = False - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -html_show_copyright = False - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -#html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -html_title = "JuliaFEM - A Finite Element Method Solver" - -# A shorter title for the navigation bar. Default is the same as html_title. -html_short_title = "JuliaFEM" - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -html_logo = 'logo/JuliaFEMLogo_96x96.png' - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -html_favicon = 'logo/JuliaFEMLogo_32x32.png' - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static', 'badges'] - -# Add any extra paths that contain custom files (such as robots.txt or -# .htaccess) here, relative to this directory. These files are copied -# directly to the root of the documentation. -#html_extra_path = [] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -html_show_sphinx = False - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Language to be used for generating the HTML full-text search index. -# Sphinx supports the following languages: -# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' -# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' -html_search_language = 'en' - -# A dictionary with options for the search language support, empty by default. -# Now only 'ja' uses this config value -#html_search_options = {'type': 'default'} - -# The name of a javascript file (relative to the configuration directory) that -# implements a search results scorer. If empty, the default will be used. -#html_search_scorer = 'scorer.js' - -# Output file base name for HTML help builder. -htmlhelp_basename = 'JuliaFEMdoc' - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', - -# Latex figure (float) alignment -#'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'JuliaFEM.tex', u'JuliaFEM Documentation', - u'Jukka Aho, Olli Väinölä, Tero Frondelius', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'juliafem', u'JuliaFEM Documentation', - [author], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'JuliaFEM', u'JuliaFEM Documentation', - author, 'JuliaFEM', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index cf3f525..0000000 --- a/docs/index.rst +++ /dev/null @@ -1,10 +0,0 @@ -.. include:: ../README.rst - -.. toctree:: - :hidden: - - self - tutorials/index - api/index - quality/index - ../CONTRIBUTING.rst diff --git a/docs/introduction.rst b/docs/introduction.rst deleted file mode 100644 index a833f4a..0000000 --- a/docs/introduction.rst +++ /dev/null @@ -1,6 +0,0 @@ -============ -Introduction -============ - -This is JuliaFEM. - diff --git a/docs/last_updated.rst b/docs/last_updated.rst deleted file mode 100644 index f9df745..0000000 --- a/docs/last_updated.rst +++ /dev/null @@ -1 +0,0 @@ -Documentation last updated (UTC): UNKNOWN diff --git a/docs/mics/links.md b/docs/mics/links.md deleted file mode 100644 index c9f7ec9..0000000 --- a/docs/mics/links.md +++ /dev/null @@ -1,22 +0,0 @@ -Discretization -============== - -http://code.activestate.com/recipes/579021-delaunay-triangulation/ - - -Interpolation -============= - -- http://www.cs.rpi.edu/~flaherje/pdf/fea4.pdf -- http://www.sd.ruhr-uni-bochum.de/downloads/Shape_funct.pdf -- http://what-when-how.com/the-finite-element-method/fem-for-3d-solids-finite-element-method-part-1/ -- http://www.uni-tuebingen.de/zag/teaching/environmental_modeling/S4B_FiniteElements.pdf -- http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.Ch10.d/AFEM.Ch10.pdf -- http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.Ch10.d/AFEM.Ch10.Slides.d/AFEM.Ch10.Slides.pdf -- http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.AppI.d/AFEM.AppI.pdf -- http://www.code-aster.org/V2/doc/default/en/man_r/r3/r3.01.01.pdf -- http://www.researchgate.net/publication/267082822_Unified_isoparametric_3D_Lagrange_finite_elements - -Integration -=========== -- http://arxiv.org/pdf/1411.1341.pdf diff --git a/docs/quality/doctests_report.rst b/docs/quality/doctests_report.rst deleted file mode 100644 index 59a2bd7..0000000 --- a/docs/quality/doctests_report.rst +++ /dev/null @@ -1,2 +0,0 @@ -This is placeholder file doc doctest results. If you see this file then doctests has not been run. - diff --git a/docs/quality/index.rst b/docs/quality/index.rst deleted file mode 100644 index 9611927..0000000 --- a/docs/quality/index.rst +++ /dev/null @@ -1,18 +0,0 @@ -Code quality -============ - -Lint report ------------ - -.. include:: lint_report.rst - -Doctest report --------------- - -.. include:: doctests_report.rst - -Unittest report ---------------- - -.. include:: unittests_report.rst - diff --git a/docs/quality/lint_report.rst b/docs/quality/lint_report.rst deleted file mode 100644 index 640cf06..0000000 --- a/docs/quality/lint_report.rst +++ /dev/null @@ -1,24 +0,0 @@ -| JuliaFEM/src/abaqus_reader.jl:7 [ ] ERROR Use of undeclared symbol level -| JuliaFEM/src/abaqus_reader.jl:34 [parse_header ] ERROR Use of undeclared symbol end -| JuliaFEM/src/abaqus_reader.jl:47 [parse_node_section] ERROR Use of undeclared symbol end -| JuliaFEM/src/abaqus_reader.jl:65 [parse_element_section] ERROR Use of undeclared symbol end -| JuliaFEM/src/abaqus_reader.jl:42 [parse_node_section] INFO Argument declared but not used: header -| JuliaFEM/src/abaqus_reader.jl:99 [process_section] INFO Argument declared but not used: section -| JuliaFEM/src/elasticity_solver.jl:7 [ ] ERROR Use of undeclared symbol level -| JuliaFEM/src/elasticity_solver.jl:71 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:72 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:78 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:94 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:98 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:99 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:105 [calc_local_matrices!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:301 [solve_elasticity_increment!] ERROR Use of undeclared symbol : -| JuliaFEM/src/elasticity_solver.jl:302 [solve_elasticity_increment!] ERROR Use of undeclared symbol : -| JuliaFEM/src/interfaces.jl:7 [ ] ERROR Use of undeclared symbol level -| JuliaFEM/src/xdmf.jl:7 [ ] ERROR Use of undeclared symbol level -| JuliaFEM/src/xdmf.jl:97 [xdmf_new_mesh ] ERROR Use of undeclared symbol : -| JuliaFEM/src/xdmf.jl:97 [xdmf_new_mesh ] ERROR Use of undeclared symbol end -| JuliaFEM/src/xdmf.jl:102 [xdmf_new_field ] INFO There is only 1 key type && 1 value type. Use explicit Dict{K,V}() for better performances. -| JuliaFEM/src/xdmf.jl:127 [xdmf_new_field ] INFO attribute is also a global, from - - Please check. diff --git a/docs/quality/unittests_report.rst b/docs/quality/unittests_report.rst deleted file mode 100644 index 559bc4e..0000000 --- a/docs/quality/unittests_report.rst +++ /dev/null @@ -1,2 +0,0 @@ -This is placeholder for unittests. This should be replaced with real report when testing. - diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 8178b81..0000000 --- a/docs/requirements.txt +++ /dev/null @@ -1 +0,0 @@ --e git+https://github.com/JuliaLang/JuliaDoc.git#egg=Julia diff --git a/docs/source/modules.rst b/docs/source/modules.rst deleted file mode 100644 index 7033b51..0000000 --- a/docs/source/modules.rst +++ /dev/null @@ -1,6 +0,0 @@ -src -=== - -.. toctree:: - :maxdepth: 4 - diff --git a/docs/mics/features.md b/docs/src/features.md similarity index 100% rename from docs/mics/features.md rename to docs/src/features.md diff --git a/docs/Type structure in JuliaFEM.mm b/docs/src/figs/Type structure in JuliaFEM.mm similarity index 100% rename from docs/Type structure in JuliaFEM.mm rename to docs/src/figs/Type structure in JuliaFEM.mm diff --git a/docs/Type structure in JuliaFEM.svg b/docs/src/figs/Type structure in JuliaFEM.svg similarity index 100% rename from docs/Type structure in JuliaFEM.svg rename to docs/src/figs/Type structure in JuliaFEM.svg diff --git a/docs/structure.dia b/docs/src/figs/structure.dia similarity index 100% rename from docs/structure.dia rename to docs/src/figs/structure.dia diff --git a/docs/structure.svg b/docs/src/figs/structure.svg similarity index 100% rename from docs/structure.svg rename to docs/src/figs/structure.svg diff --git a/docs/links.md b/docs/src/links.md similarity index 100% rename from docs/links.md rename to docs/src/links.md diff --git a/docs/mics/2015-05-23-one-element-solution.ipynb b/docs/tutorials/2015-05-23-one-element-solution.ipynb similarity index 100% rename from docs/mics/2015-05-23-one-element-solution.ipynb rename to docs/tutorials/2015-05-23-one-element-solution.ipynb diff --git a/notebooks/2015-06-25-elasticity-solver-example.ipynb b/docs/tutorials/2015-06-25-elasticity-solver-example.ipynb similarity index 100% rename from notebooks/2015-06-25-elasticity-solver-example.ipynb rename to 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