Skip to content

Commit

Permalink
Merge pull request #5484 from openjournals/joss.06599
Browse files Browse the repository at this point in the history 
Merging automatically
  • Loading branch information
@editorialbot
editorialbot authored Jun 11, 2024
2 parents 61b2256 + ec4523f commit d6200e3
Show file tree
Hide file tree
Showing 4 changed files with 1,016 additions and 0 deletions.
364 changes: 364 additions & 0 deletions joss.06599/10.21105.joss.06599.crossref.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,364 @@
<?xml version="1.0" encoding="UTF-8"?>
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1"
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd"
xmlns:rel="http://www.crossref.org/relations.xsd"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
version="5.3.1"
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd">
<head>
<doi_batch_id>20240611141725-2fa4361969da6896aa852c481472d7f2e6b156e6</doi_batch_id>
<timestamp>20240611141725</timestamp>
<depositor>
<depositor_name>JOSS Admin</depositor_name>
<email_address>[email protected]</email_address>
</depositor>
<registrant>The Open Journal</registrant>
</head>
<body>
<journal>
<journal_metadata>
<full_title>Journal of Open Source Software</full_title>
<abbrev_title>JOSS</abbrev_title>
<issn media_type="electronic">2475-9066</issn>
<doi_data>
<doi>10.21105/joss</doi>
<resource>https://joss.theoj.org</resource>
</doi_data>
</journal_metadata>
<journal_issue>
<publication_date media_type="online">
<month>06</month>
<year>2024</year>
</publication_date>
<journal_volume>
<volume>9</volume>
</journal_volume>
<issue>98</issue>
</journal_issue>
<journal_article publication_type="full_text">
<titles>
<title>ComFiT: a Python library for computational field theory
with topological defects</title>
</titles>
<contributors>
<person_name sequence="first" contributor_role="author">
<given_name>Vidar</given_name>
<surname>Skogvoll</surname>
<ORCID>https://orcid.org/0000-0003-4941-6886</ORCID>
</person_name>
<person_name sequence="additional"
contributor_role="author">
<given_name>Jonas</given_name>
<surname>Rønning</surname>
<ORCID>https://orcid.org/0000-0001-5289-7276</ORCID>
</person_name>
</contributors>
<publication_date>
<month>06</month>
<day>11</day>
<year>2024</year>
</publication_date>
<pages>
<first_page>6599</first_page>
</pages>
<publisher_item>
<identifier id_type="doi">10.21105/joss.06599</identifier>
</publisher_item>
<ai:program name="AccessIndicators">
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
</ai:program>
<rel:program>
<rel:related_item>
<rel:description>Software archive</rel:description>
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.11395524</rel:inter_work_relation>
</rel:related_item>
<rel:related_item>
<rel:description>GitHub review issue</rel:description>
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/6599</rel:inter_work_relation>
</rel:related_item>
</rel:program>
<doi_data>
<doi>10.21105/joss.06599</doi>
<resource>https://joss.theoj.org/papers/10.21105/joss.06599</resource>
<collection property="text-mining">
<item>
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.06599.pdf</resource>
</item>
</collection>
</doi_data>
<citation_list>
<citation key="mazenkoVortexVelocitiesSymmetric1997">
<article_title>Vortex velocities in the O(n) symmetric
time-dependent ginzburg-landau model</article_title>
<author>Mazenko</author>
<journal_title>Phys. Rev. Lett.</journal_title>
<issue>3</issue>
<volume>78</volume>
<doi>10.1103/PhysRevLett.78.401</doi>
<cYear>1997</cYear>
<unstructured_citation>Mazenko, G. F. (1997). Vortex
velocities in the O(n) symmetric time-dependent ginzburg-landau model.
Phys. Rev. Lett., 78(3), 401–404.
https://doi.org/10.1103/PhysRevLett.78.401</unstructured_citation>
</citation>
<citation key="mazenkoVelocityDistributionStrings1999">
<article_title>Velocity distribution for strings in
phase-ordering kinetics</article_title>
<author>Mazenko</author>
<journal_title>Physical Review E</journal_title>
<issue>2</issue>
<volume>59</volume>
<doi>10.1103/PhysRevE.59.1574</doi>
<cYear>1999</cYear>
<unstructured_citation>Mazenko, G. F. (1999). Velocity
distribution for strings in phase-ordering kinetics. Physical Review E,
59(2), 1574–1584.
https://doi.org/10.1103/PhysRevE.59.1574</unstructured_citation>
</citation>
<citation key="anghelutaAnisotropicVelocityStatistics2012">
<article_title>Anisotropic velocity statistics of
topological defects under shear flow</article_title>
<author>Angheluta</author>
<journal_title>Phys. Rev. E</journal_title>
<issue>1</issue>
<volume>85</volume>
<doi>10.1103/PhysRevE.85.011153</doi>
<cYear>2012</cYear>
<unstructured_citation>Angheluta, L., Jeraldo, P., &amp;
Goldenfeld, N. (2012). Anisotropic velocity statistics of topological
defects under shear flow. Phys. Rev. E, 85(1), 011153.
https://doi.org/10.1103/PhysRevE.85.011153</unstructured_citation>
</citation>
<citation key="coxExponentialTimeDifferencing2002">
<article_title>Exponential Time Differencing for Stiff
Systems</article_title>
<author>Cox</author>
<journal_title>Journal of Computational
Physics</journal_title>
<issue>2</issue>
<volume>176</volume>
<doi>10.1006/jcph.2002.6995</doi>
<issn>0021-9991</issn>
<cYear>2002</cYear>
<unstructured_citation>Cox, S. M., &amp; Matthews, P. C.
(2002). Exponential Time Differencing for Stiff Systems. Journal of
Computational Physics, 176(2), 430–455.
https://doi.org/10.1006/jcph.2002.6995</unstructured_citation>
</citation>
<citation key="skaugenUnifiedPerspectiveTwodimensional2018">
<article_title>A unified perspective on two-dimensional
quantum turbulence and plasticity</article_title>
<author>Skaugen</author>
<cYear>2018</cYear>
<unstructured_citation>Skaugen, A. (2018). A unified
perspective on two-dimensional quantum turbulence and plasticity [PhD
thesis]. The University of Oslo;
https://www.duo.uio.no/handle/10852/66179.</unstructured_citation>
</citation>
<citation key="skogvollDislocationNucleationPhasefield2021">
<article_title>Dislocation nucleation in the phase-field
crystal model</article_title>
<author>Skogvoll</author>
<journal_title>Physical Review B</journal_title>
<issue>1</issue>
<volume>103</volume>
<doi>10.1103/PhysRevB.103.014107</doi>
<cYear>2021</cYear>
<unstructured_citation>Skogvoll, V., Skaugen, A., Angheluta,
L., &amp; Viñals, J. (2021). Dislocation nucleation in the phase-field
crystal model. Physical Review B, 103(1), 014107.
https://doi.org/10.1103/PhysRevB.103.014107</unstructured_citation>
</citation>
<citation key="skogvollStressOrderedSystems2021">
<article_title>Stress in ordered systems:
Ginzburg-Landau-type density field theory</article_title>
<author>Skogvoll</author>
<journal_title>Physical Review B</journal_title>
<issue>22</issue>
<volume>103</volume>
<doi>10.1103/PhysRevB.103.224107</doi>
<cYear>2021</cYear>
<unstructured_citation>Skogvoll, V., Skaugen, A., &amp;
Angheluta, L. (2021). Stress in ordered systems: Ginzburg-Landau-type
density field theory. Physical Review B, 103(22), 224107.
https://doi.org/10.1103/PhysRevB.103.224107</unstructured_citation>
</citation>
<citation key="skogvollPhaseFieldCrystal2022">
<article_title>A phase field crystal theory of the
kinematics of dislocation lines</article_title>
<author>Skogvoll</author>
<journal_title>Journal of the Mechanics and Physics of
Solids</journal_title>
<volume>166</volume>
<doi>10.1016/j.jmps.2022.104932</doi>
<issn>0022-5096</issn>
<cYear>2022</cYear>
<unstructured_citation>Skogvoll, V., Angheluta, L., Skaugen,
A., Salvalaglio, M., &amp; Viñals, J. (2022). A phase field crystal
theory of the kinematics of dislocation lines. Journal of the Mechanics
and Physics of Solids, 166, 104932.
https://doi.org/10.1016/j.jmps.2022.104932</unstructured_citation>
</citation>
<citation key="skogvollHydrodynamicPhaseField2022">
<article_title>Hydrodynamic phase field crystal approach to
interfaces, dislocations and multi-grain networks</article_title>
<author>Skogvoll</author>
<journal_title>Modelling and Simulation in Materials Science
and Engineering</journal_title>
<doi>10.1088/1361-651X/ac9493</doi>
<issn>0965-0393</issn>
<cYear>2022</cYear>
<unstructured_citation>Skogvoll, V., Salvalaglio, M., &amp;
Angheluta, L. (2022). Hydrodynamic phase field crystal approach to
interfaces, dislocations and multi-grain networks. Modelling and
Simulation in Materials Science and Engineering.
https://doi.org/10.1088/1361-651X/ac9493</unstructured_citation>
</citation>
<citation key="skogvollUnifiedFieldTheory2023">
<article_title>A unified field theory of topological defects
and non-linear local excitations</article_title>
<author>Skogvoll</author>
<journal_title>npj Computational Materials</journal_title>
<issue>1</issue>
<volume>9</volume>
<doi>10.1038/s41524-023-01077-6</doi>
<issn>2057-3960</issn>
<cYear>2023</cYear>
<unstructured_citation>Skogvoll, V., Rønning, J.,
Salvalaglio, M., &amp; Angheluta, L. (2023). A unified field theory of
topological defects and non-linear local excitations. Npj Computational
Materials, 9(1), 1–13.
https://doi.org/10.1038/s41524-023-01077-6</unstructured_citation>
</citation>
<citation key="skogvollSymmetryTopologyCrystal2023">
<article_title>Symmetry, topology, and crystal deformations:
A phase-field crystal approach</article_title>
<author>Skogvoll</author>
<cYear>2023</cYear>
<unstructured_citation>Skogvoll, V. (2023). Symmetry,
topology, and crystal deformations: A phase-field crystal approach [PhD
thesis].
https://www.duo.uio.no/handle/10852/102731.</unstructured_citation>
</citation>
<citation key="ronningTopologicalDefectsFlows2023">
<article_title>Topological Defects and Flows in BECs and
Active Matter</article_title>
<author>Rønning</author>
<cYear>2023</cYear>
<unstructured_citation>Rønning, J. (2023). Topological
Defects and Flows in BECs and Active Matter [PhD thesis].
https://www.duo.uio.no/handle/10852/104678.</unstructured_citation>
</citation>
<citation key="ronningSpontaneousFlowsDynamics2023">
<article_title>Spontaneous flows and dynamics of
full-integer topological defects in polar active matter</article_title>
<author>Rønning</author>
<journal_title>Soft Matter</journal_title>
<issue>39</issue>
<volume>19</volume>
<doi>10.1039/D3SM00316G</doi>
<issn>1744-6848</issn>
<cYear>2023</cYear>
<unstructured_citation>Rønning, J., Renaud, J.,
Doostmohammadi, A., &amp; Angheluta, L. (2023). Spontaneous flows and
dynamics of full-integer topological defects in polar active matter.
Soft Matter, 19(39), 7513–7527.
https://doi.org/10.1039/D3SM00316G</unstructured_citation>
</citation>
<citation key="ronningClassicalAnalogiesForce2020">
<article_title>Classical analogies for the force acting on
an impurity in a Bose–Einstein condensate</article_title>
<author>Rønning</author>
<journal_title>New Journal of Physics</journal_title>
<issue>7</issue>
<volume>22</volume>
<doi>10.1088/1367-2630/ab95de</doi>
<issn>1367-2630</issn>
<cYear>2020</cYear>
<unstructured_citation>Rønning, J., Skaugen, A.,
Hernández-García, E., Lopez, C., &amp; Angheluta, L. (2020). Classical
analogies for the force acting on an impurity in a Bose–Einstein
condensate. New Journal of Physics, 22(7), 073018.
https://doi.org/10.1088/1367-2630/ab95de</unstructured_citation>
</citation>
<citation key="ronningPrecursoryPatternsVortex2023">
<article_title>Precursory patterns to vortex nucleation in
stirred Bose-Einstein condensates</article_title>
<author>Rønning</author>
<journal_title>Physical Review Research</journal_title>
<issue>2</issue>
<volume>5</volume>
<doi>10.1103/PhysRevResearch.5.023108</doi>
<cYear>2023</cYear>
<unstructured_citation>Rønning, J., &amp; Angheluta, L.
(2023). Precursory patterns to vortex nucleation in stirred
Bose-Einstein condensates. Physical Review Research, 5(2), 023108.
https://doi.org/10.1103/PhysRevResearch.5.023108</unstructured_citation>
</citation>
<citation key="alnaesFEniCSProjectVersion2015">
<article_title>The FEniCS project version
1.5</article_title>
<author>Alnaes</author>
<journal_title>Archive of Numerical Software</journal_title>
<volume>3</volume>
<doi>10.11588/ans.2015.100.20553</doi>
<cYear>2015</cYear>
<unstructured_citation>Alnaes, M. S., Blechta, J., Hake, J.,
Johansson, A., Kehlet, B., Logg, A., Richardson, C. N., Ring, J.,
Rognes, M. E., &amp; Wells, G. N. (2015). The FEniCS project version
1.5. Archive of Numerical Software, 3.
https://doi.org/10.11588/ans.2015.100.20553</unstructured_citation>
</citation>
<citation key="ketchesonPyClawAccessibleExtensible2012">
<article_title>PyClaw: Accessible, extensible, scalable
tools for wave propagation problems</article_title>
<author>Ketcheson</author>
<journal_title>SIAM Journal on Scientific
Computing</journal_title>
<issue>4</issue>
<volume>34</volume>
<doi>10.1137/110856976</doi>
<cYear>2012</cYear>
<unstructured_citation>Ketcheson, D. I., Mandli, K. T.,
Ahmadia, A. J., Alghamdi, A., Quezada de Luna, M., Parsani, M., Knepley,
M. G., &amp; Emmett, M. (2012). PyClaw: Accessible, extensible, scalable
tools for wave propagation problems. SIAM Journal on Scientific
Computing, 34(4), C210–C231.
https://doi.org/10.1137/110856976</unstructured_citation>
</citation>
<citation key="hamFiredrakeUserManual2023">
<volume_title>Firedrake user manual</volume_title>
<author>Ham</author>
<doi>10.25561/104839</doi>
<cYear>2023</cYear>
<unstructured_citation>Ham, D. A., Kelly, P. H. J.,
Mitchell, L., Cotter, C. J., Kirby, R. C., Sagiyama, K., Bouziani, N.,
Vorderwuelbecke, S., Gregory, T. J., Betteridge, J., Shapero, D. R.,
Nixon-Hill, R. W., Ward, C. J., Farrell, P. E., Brubeck, P. D., Marsden,
I., Gibson, T. H., Homolya, M., Sun, T., … Markall, G. R. (2023).
Firedrake user manual (First edition) [Manual]. Imperial College London
and University of Oxford and Baylor University and University of
Washington. https://doi.org/10.25561/104839</unstructured_citation>
</citation>
<citation key="burnsDedalusFlexibleFramework2020">
<article_title>Dedalus: A flexible framework for numerical
simulations with spectral methods</article_title>
<author>Burns</author>
<journal_title>Physical Review Research</journal_title>
<issue>023068</issue>
<volume>2</volume>
<doi>10.1103/PhysRevResearch.2.023068</doi>
<cYear>2020</cYear>
<unstructured_citation>Burns, K. J., Vasil, G. M., Oishi, J.
S., Lecoanet, D., &amp; Brown, B. P. (2020). Dedalus: A flexible
framework for numerical simulations with spectral methods. Physical
Review Research, 2(023068), 023068.
https://doi.org/10.1103/PhysRevResearch.2.023068</unstructured_citation>
</citation>
</citation_list>
</journal_article>
</journal>
</body>
</doi_batch>
Binary file added joss.06599/10.21105.joss.06599.pdf
View file
Binary file not shown.
Loading

0 comments on commit d6200e3

Please sign in to comment.