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Merge pull request #931 from festim-dev/update-docs
Update docs on fenicsx
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‎.github/workflows/doctest.yml‎

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name: Documentation test
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on: [push, pull_request]
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jobs:
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docbuild:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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- name: Set up Conda
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uses: conda-incubator/setup-miniconda@v2
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with:
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activate-environment: festim2-docs
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environment-file: docs/environment.yml
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- name: Doc Tests
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shell: bash -l {0}
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run: sphinx-build -b doctest docs/source docs/_build/doctest

‎.readthedocs.yaml‎

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version: 2
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conda:
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environment: docs/source/environment.yaml
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environment: docs/environment.yml
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build:
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os: "ubuntu-20.04"
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration: docs/source/conf.py
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# If using Sphinx, optionally build your docs in additional formats such as PDF
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# formats:
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# - pdf
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# # Optionally declare the Python requirements required to build your docs
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python:
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install:
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- method: pip
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path: .
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# python:
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# install:
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# - requirements: docs/requirements.txt

‎docs/environment.yml‎

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name: festim2-docs
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channels:
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- conda-forge
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- defaults
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dependencies:
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- fenics-dolfinx
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- matplotlib==3.7.1
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- pip>=20.1
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- sphinx<8 # sphinxcontrib-images is not compatible with sphinx 8
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- folium
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- numpy==1.24
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- tqdm
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- scifem>=0.2.8
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- sphinx-design
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- sphinxcontrib-bibtex
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- sphinxcontrib-images
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- sympy
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- sphinx-book-theme
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- sphinx-copybutton
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- pillow

‎docs/source/Makefile‎

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/source/_static/style.css‎

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@import url('https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;0,900;1,400;1,700;1,900&family=Open+Sans:ital,wght@0,400;0,600;1,400;1,600&display=swap');
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body {
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font-family: 'Open Sans', sans-serif;
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}
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h1 {
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font-family: "Lato", sans-serif;
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}
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pre,
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code {
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font-size: 100%;
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line-height: 155%;
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}
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/* Main page overview cards */
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.sd-card {
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border-radius: 0;
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padding: 30px 10px 20px 10px;
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margin: 10px 0px;
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}
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.sd-card .sd-card-header {
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text-align: center;
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}
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.sd-card .sd-card-title {
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text-align: center;
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}
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.sd-card .sd-card-header .sd-card-text {
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margin: 0px;
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}
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.sd-card .sd-card-img-top {
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height: 52px;
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width: 52px;
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margin-left: auto;
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margin-right: auto;
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}
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.sd-card .sd-card-header {
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border: none;
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font-size: var(--pst-font-size-h5);
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font-weight: bold;
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padding: 2.5rem 0rem 0.5rem 0rem;
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}
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/*
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SPHINX-BOOK-THEME HOTFIX (top-right icons):
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https://github.com/executablebooks/sphinx-book-theme/issues/879
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*/
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.header-article__inner .header-article-items__end,
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.header-article__inner .header-article-items__start {
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align-items: start;
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display: flex;
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gap: .5rem;
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}
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/*
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SPHINX-BOOK-THEME HOTFIX (right column vertical stretching fix):
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https://github.com/executablebooks/sphinx-book-theme/issues/879
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*/
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.toc-entry a.nav-link {
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padding: .125rem 0 .125rem 1rem;
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}
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/*
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h3 font weight fix (from extra heavy to normal):
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https://github.com/executablebooks/sphinx-book-theme/issues/879
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*/
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h3 {
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font-size: 125%;
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font-weight: normal;
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}

‎docs/source/api/index.rst‎

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FESTIM API
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==========
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.. warning::
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🔨 This page is under construction. 🔨
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.. automodule:: festim.boundary_conditions
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:members:

‎docs/source/bibliography/references.bib‎

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@article{McNabb1963,
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title = {{A New Analysis of the Diffusion of Hydrogen in Iron and Ferritic Steels}},
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author = {McNabb, A. and Foster, P. K.},
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year = 1963,
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journal = {Trans. Metall. Soc. AIME},
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volume = 227,
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pages = 618
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}
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@article{Longhurst1985,
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title = {{The soret effect and its implications for fusion reactors}},
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author = {Longhurst, G. R.},
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year = 1985,
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journal = {J. Nucl. Mater.},
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volume = 131,
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number = 1,
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pages = {61--69},
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issn = {00223115},
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url = {https://linkinghub.elsevier.com/retrieve/pii/0022311585904258}
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}
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@techreport{Pendergrass1976,
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title = {{Temperature-dependent ordinary and thermal diffusion of hydrogen isotopes through thermonuclear reactor components}},
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author = {Pendergrass, J. H.},
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year = 1976,
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url = {http://www.osti.gov/servlets/purl/7333557/},
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institution = {Los Alamos National Laboratory (LANL)}
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}
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@article{Delaporte-Mathurin2021,
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title = {{Influence of interface conditions on hydrogen transport studies}},
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author = {Delaporte-Mathurin, R. and Hodille, E. A. and Mougenot, J. and Charles, Y. and {De Temmerman}, G. and Leblond, F. and Grisolia, C.},
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year = 2021,
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journal = {Nucl. Fusion},
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volume = 61,
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number = 3,
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pages = {036038},
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issn = {0029-5515},
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url = {https://iopscience.iop.org/article/10.1088/1741-4326/abd95f}
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}
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@phdthesis{Delaporte-Mathurin2022,
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title = {{Hydrogen transport in tokamaks : Estimation of the ITER divertor tritium inventory and influence of helium exposure}},
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author = {Delaporte-Mathurin, R.},
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year = 2022,
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number = {2022PA131054},
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url = {https://theses.hal.science/tel-04004369},
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school = {{Universit{\'e} Paris-Nord - Paris XIII}},
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keywords = {Hydrogen ; Finite elements ; Numerical modelling ; Hydrog{\`e}ne ; El{\'e}ments finis ; Mod{\'e}lisation num{\'e}rique},
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type = {Theses}
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}
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@article{Schmid2016,
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title = {{Diffusion-trapping modelling of hydrogen recycling in tungsten under ELM-like heat loads}},
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author = {Schmid, K.},
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year = 2016,
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journal = {Phys. Scr.},
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volume = {T167},
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pages = {014025},
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issn = {0031-8949},
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url = {https://iopscience.iop.org/article/10.1088/0031-8949/T167/1/014025}
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}
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@article{Guterl2019,
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title = {Effects of surface processes on hydrogen outgassing from metal in desorption experiments},
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author = {Guterl, Jerome and Smirnov, RD and Snyder, P},
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year = 2019,
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journal = {Nuclear Fusion},
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publisher = {IOP Publishing},
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volume = 59,
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number = 9,
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pages = {096042},
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url = {https://iopscience.iop.org/article/10.1088/1741-4326/ab280a/meta}
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}
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@article{Pick1985,
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title = {A model for atomic hydrogen-metal interactions—application to recycling, recombination and permeation},
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author = {Pick, MA and Sonnenberg, K},
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year = 1985,
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journal = {Journal of Nuclear Materials},
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publisher = {Elsevier},
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volume = 131,
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number = {2-3},
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pages = {208--220},
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url = {https://www.sciencedirect.com/science/article/abs/pii/0022311585904593}
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}
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@article{Hodille2017,
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title = {Simulations of atomic deuterium exposure in self-damaged tungsten},
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author = {Hodille, EA and Zalo{\v{z}}nik, A and Markelj, S and Schwarz-Selinger, T and Becquart, CS and Bisson, R{\'e}gis and Grisolia, Christian},
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year = 2017,
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journal = {Nuclear Fusion},
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publisher = {IOP Publishing},
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volume = 57,
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number = 5,
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pages = {056002},
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url = {https://iopscience.iop.org/article/10.1088/1741-4326/aa5aa5/meta}
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}
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@article{Schmid2021,
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title = {On the use of recombination rate coefficients in hydrogen transport calculations},
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author = {Schmid, K and Zibrov, M},
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year = 2021,
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journal = {Nuclear Fusion},
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publisher = {IOP Publishing},
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volume = 61,
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number = 8,
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pages = {086008},
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url = {https://iopscience.iop.org/article/10.1088/1741-4326/ac07b2/meta}
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}
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@article{Hamamoto2020,
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title = {Comprehensive modeling of hydrogen transport and accumulation in titanium and zirconium},
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author = {Hamamoto, Yoshiki and Uchikoshi, Takeru and Tanabe, Katsuaki},
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year = 2020,
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journal = {Nuclear Materials and Energy},
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publisher = {Elsevier},
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volume = 23,
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pages = 100751,
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url = {https://www.sciencedirect.com/science/article/pii/S2352179120300272}
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}

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