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Merge pull request #209 from missing-user/readme-404-fix
Readme 404 fix
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‎.github/workflows/doxygen.yml

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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v2
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# Validate CITATION.cff
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- name: CITATION.cff to spec_refs.bib
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run: |
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pip install --user pyyaml cffconvert==2.0.0
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cffconvert --validate
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# run doxygen
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- name: Doxygen Action
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uses: mattnotmitt/[email protected]
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- name: Copy Pdf
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working-directory: ${{ github.workspace }}
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run: sudo cp ./docs/latex/refman.pdf ./docs/html/SPEC_manual.pdf
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run: |
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sudo cp ./docs/latex/refman.pdf ./docs/html/SPEC_manual.pdf
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sudo cp ./docs/SPEC_flowchart.pdf ./docs/html/SPEC_flowchart.pdf
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3

‎CITATION.cff

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cff-version: 1.2.0
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title: Stepped Pressure Equilibrium Code (SPEC)
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message: If you use SPEC in your research, please cite the following works.
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type: software
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contact:
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- family-names: Hudson
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given-names: Stuart
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email: [email protected]
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affiliation: Princeton Plasma Physics Laboratory
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orcid: "https://orcid.org/0000-0003-1530-2733"
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authors:
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- family-names: Hudson
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given-names: Stuart
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email: [email protected]
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affiliation: Princeton Plasma Physics Laboratory
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orcid: "https://orcid.org/0000-0003-1530-2733"
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- family-names: Schilling
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given-names: Jonathan
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affiliation: Max-Planck Institute for Plasma Physics
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orcid: https://orcid.org/0000-0002-6363-6554
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- family-names: Baillod
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given-names: Antoine
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affiliation: Columbia University
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orcid: https://orcid.org/0000-0003-0352-9180
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- family-names: Qu
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given-names: Zhisong
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affiliation: Nanyang Technological University
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orcid: https://orcid.org/0000-0003-4628-6983
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- family-names: Loizu
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given-names: Joaquim
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affiliation: Federal Institute of Technology Lausanne (EPFL)
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orcid: https://orcid.org/0000-0002-4862-7393
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- family-names: Medasani
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given-names: Bharat
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affiliation: New Mexico State University
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- family-names: Smiet
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given-names: Christopher Berg
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orcid: https://orcid.org/0000-0002-7803-7685
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affiliation: Federal Institute of Technology Lausanne (EPFL)
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- family-names: Zhu
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given-names: Caoxiang
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affiliation: University of Science and Technology of China
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orcid: https://orcid.org/0000-0003-2337-3232
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- family-names: Lazerson
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given-names: Samuel Aaron
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affiliation: Princeton Plasma Physics Laboratory
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orcid: https://orcid.org/0000-0001-8002-0121
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- family-names: Breslau
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given-names: Joshua
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affiliation: Princeton Plasma Physics Laboratory
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orcid: https://orcid.org/0000-0002-0649-4836
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identifiers:
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- type: url
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value: https://github.com/PrincetonUniversity/SPEC/releases/tag/v3.20
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description: The GitHub URL for the SPEC v3.20 release
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repository-code: https://github.com/PrincetonUniversity/SPEC
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url: https://princetonuniversity.github.io/SPEC/
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abstract: >-
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A code for calculating magnetohydrodynamic equilibria with
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stepped pressure-profiles, by finding stationary points in
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the MRxMHD energy functional.
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keywords:
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- magnetohydrodynamics
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- SPEC
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- MRxMHD
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license: GPL-3.0
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commit: 5996ea6db8cea383c659fced8e6a2c24cd774642
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version: "3.20"
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date-released: "2022-07-01"
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preferred-citation:
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type: article
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authors:
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- family-names: Hudson
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given-names: Stuart
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email: [email protected]
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affiliation: "Princeton Plasma Physics Laboratory"
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orcid: "https://orcid.org/0000-0003-1530-2733"
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- family-names: Dewar
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given-names: R. L.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: Hole
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given-names: M. J.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: Dennis
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given-names: G.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: McGann
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given-names: M.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: von Nessi
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given-names: G.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: Lazerson
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given-names: Samuel Aaron
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affiliation: "Princeton Plasma Physics Laboratory"
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orcid: https://orcid.org/0000-0001-8002-0121
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title: Computation of multi-region relaxed magnetohydrodynamic equilibria
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journal: Phys. Plasmas
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volume: "19"
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issue: "11"
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year: 2012
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doi: 10.1063/1.4765691
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url: "https://doi.org/10.1063/1.4765691"
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references:
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- type: article
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authors:
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- family-names: Hudson
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given-names: Stuart
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email: [email protected]
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affiliation: "Princeton Plasma Physics Laboratory"
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orcid: "https://orcid.org/0000-0003-1530-2733"
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- family-names: Dewar
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given-names: R. L.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: Hole
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given-names: M. J.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: Dennis
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given-names: G.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: McGann
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given-names: M.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: von Nessi
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given-names: G.
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affiliation: "Plasma Research Laboratory, Research School of Physics & Engineering, The Australian National University, Canberra ACT 0200, Australia"
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- family-names: Lazerson
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given-names: Samuel Aaron
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affiliation: "Princeton Plasma Physics Laboratory"
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orcid: https://orcid.org/0000-0001-8002-0121
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title: Computation of multi-region relaxed magnetohydrodynamic equilibria
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journal: Phys. Plasmas
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volume: "19"
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issue: "11"
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year: 2012
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doi: 10.1063/1.4765691
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url: "https://doi.org/10.1063/1.4765691"
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- type: article
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authors:
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- family-names: Hudson
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given-names: Stuart R.
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orcid: https://orcid.org/0000-0003-1530-2733
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- family-names: Loizu
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given-names: Joaquim
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orcid: https://orcid.org/0000-0002-4862-7393
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- family-names: Zhu
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given-names: Caoxiang
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orcid: https://orcid.org/0000-0003-2337-3232
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- family-names: Qu
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given-names: Zhisong
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orcid: https://orcid.org/0000-0003-4628-6983
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- family-names: Nührenberg
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given-names: Carolin
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- family-names: Lazerson
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given-names: Samuel A.
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orcid: https://orcid.org/0000-0001-8002-0121
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- family-names: Smiet
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given-names: Christopher Berg
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orcid: https://orcid.org/0000-0002-7803-7685
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- family-names: Hole
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given-names: Matthew J.
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orcid: https://orcid.org/0000-0002-9550-8776
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title: "Free-boundary MRxMHD equilibrium calculations using the stepped-pressure equilibrium code"
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journal: "Plasma Physics and Controlled Fusion"
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volume: "62"
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issue: "8"
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pages: "084002"
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year: 2020
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doi: "10.1088/1361-6587/ab9a61"
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url: "https://dx.doi.org/10.1088/1361-6587/ab9a61"
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‎Doxyfile

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# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
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# Note: If this tag is empty the current directory is searched.
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INPUT = README.md Compile.md src
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INPUT = README.md compilation_instructions.md src docs/Citelist.md
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# This tag can be used to specify the character encoding of the source files
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# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

‎README.md

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# The Stepped Pressure Equilibrium Code
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![SPEC logo](SPEC_97x55.png)
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# The Stepped Pressure Equilibrium Code
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All relevant publications and presentations are given on the [MRxMHD website](http://w3.pppl.gov/~shudson/Spec/spec.html).
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SPEC solves 3D magnetohydrodynamic (MHD) equilibria with stepped-pressure profiles. This powerful description doesn't artificially restrict the solution to nested flux surfaces, and admits simulations with islands and chaotic regions. It is a spectral-element code, that finds minimal-plasma-energy states by extremizing the multi-region, relaxed-MHD (MRxMHD) energy functional.
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A BibTex file is available: [spec_refs.bib](https://raw.githubusercontent.com/PrincetonUniversity/SPEC/master/spec_refs.bib).
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- There is a [brief description of SPEC](https://theory.pppl.gov/research/research.php?rid=10#h5) on the Princeton Plasma Physics Laboratory [Theory Department website](https://theory.pppl.gov/).
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- An overview of the algorithm is given in a [Flow Chart](https://princetonuniversity.github.io/SPEC/docs/SPEC_flowchart.pdf).
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- A list of publications using SPEC are in our [bibliography section](https://princetonuniversity.github.io/SPEC/citelist)
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- Please direct questions/suggestions to [Stuart Hudson](mailto:[email protected]?subject=spec).
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## Citation
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If you use SPEC in your research, please cite it appropriately using the "Cite this repository" button on the right of the [SPEC GitHub Repository](https://github.com/PrincetonUniversity/SPEC) or the [CITATION.cff](https://github.com/PrincetonUniversity/SPEC/blob/master/CITATION.cff) file.
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## Installation
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Instructions for compiling and testing SPEC are in [compilation_instructions.md](compilation_instructions.md).
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## Documentation
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Online documentation for SPEC is available on [Github pages](https://princetonuniversity.github.io/SPEC/) or in PDF form at [SPEC_manual.pdf](https://princetonuniversity.github.io/SPEC/SPEC_manual.pdf).
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* There is also a [brief description of SPEC](http://theory.pppl.gov/research/research.php?rid=10#h5)
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on the Princeton Plasma Physics Laboratory [Theory Department website](http://theory.pppl.gov/).
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* An overview of the algorithm is given in a [Flow Chart](http://w3.pppl.gov/~shudson/Spec/SpecFlowchart.pdf).
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* Please direct questions/suggestions to [Stuart Hudson](mailto:[email protected]?subject=spec).
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* Online documentation for SPEC is available on [Github pages](https://princetonuniversity.github.io/SPEC/).
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A PDF version of this manual is available in [SPEC_manual.pdf](https://princetonuniversity.github.io/SPEC/SPEC_manual.pdf).
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* Instructions for compiling and testing SPEC are in [Compile.md](https://github.com/PrincetonUniversity/SPEC/blob/master/Compile.md).

‎docs/Citelist.md

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List of papers using spec
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(Citations that aren't explicitly referenced, don't appear in the bibliography, so we list them all here.)
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\cite y2015_hanson
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\cite y2017_zhu
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\cite y2016_loizu
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\cite y2021_baillod
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\cite y2016_loizu_1
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\cite y2015_loizu_1
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\cite y2015_loizu
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\cite y2020_loizu
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\cite y2023_loizu
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\cite y2017_loizu
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\cite y2023_baillod
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\cite y2019_loizu
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\cite y2024_liu

‎docs/SPEC_flowchart.pdf

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