SPECFEM
Replies: 22 comments 25 replies
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Also, we need a headshot image and banner image for the google scholar page. The attachment show what it looks like now. It also shows the button that the "pubs lead" can click in order to add articles. Google is efficient about finding sets of similar articles to review for adding into the profile.
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Added |
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One way to make this easier is to remind people to cite SPECFEM in their paper. I have google scholar searches set up that captures most(?). See the landing pages for the software pages on geodynamics.org for these. |
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Where is the list of citations? I could not easily find it from the landing page you linked. Thanks. |
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https://geodynamics.org/resources/specfem3d/citations Note that this includes geotech which has not been moved. This should be moved also to this repo. It looks orphaned where it is. If you setup your own google search, be a bit careful on searching on one term as not all terms are unique and referencing the recommended publications does not always mean they use the software. |
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Thanks, Lorraine. Hopefully someone can comb these existing lists and make sure that they are included in the google scholar profile. |
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Thanks, @ljhwang and @jpampuero for the article lists. I'll start my turn as publication Czar by reviewing and adding from these compilations. -Brandon |
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Has anyone ever tried to embed zotero into a website? I am wondering if there is a way to crowd source the effort! |
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This is an interesting idea that I can look into. This also made me think about creating a citation tree from the seminal specfem papers or a graph similar to those produced via connectedpapers.com to visually illustrate the influence of specfem in the broader seismologic community. |
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We do something similar but look at coAuthor networks to show how research networks grow and why it is good to contribute code to a project! Here is a particularly complex example from the deal.ii project
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Here's another one: |
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Added! |
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Thanks Amanda. I see where I have been missing references. I had thought that standardly the Komatatisch & Tromp article9s) is cited. I see here that Peters et al. 2011 is the only publication cited in this article. Are there other publications typically cited? This will help my google alert searches. |
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again |
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Added except this one (https://doi.org10.1002/ggge.20081) because link is broken; please provide article title or new link. |
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Correct |
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Added. |
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A few more specfem papers below:
https://doi.org/10.1121/1.3682459
https://doi.org/10.1121/1.4965964
https://doi.org/10.1016/j.ndteint.2018.10.002
https://doi.org/10.1121/1.4989349
https://link.springer.com/article/10.1007/s00024-020-02611-z
https://doi.org/10.1121/1.5055787
https://doi.org/10.1121/10.0009610
https://doi.org/10.1121/10.0012219
Thank you!
Alexis
…On Tue, Nov 8, 2022 at 1:52 AM emanuele casarotti ***@***.***> wrote:
again
http://dx.doi.org/10.1016/j.epsl.2017.04.017
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Added! |
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Hi @bvanderbeek, thanks for taking over the task! I combed through Carl's original list and checked if they are specfem related or not. Please double check again when you go through them:
One paper missing from Dimitri's publication:
Another one missing:
Some papers missing from Min Chen's publications:
Here are a few missing with our group as co-authors:
Also it seems the specfem google scholar can only sort the publications in reverse chronological order, not the forward order. |
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Removed/added |
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Big thanks to @bvanderbeek for pushing this forward. My gut feeling is that we probably have <50% or so of the specfem papers listed in the profile. In some cases, we may never know, since the paper may not acknowledge the use of specfem. Many others to be found are likely among the pile of 22,000 papers that are citing the yes-we-used-specfem papers. At this stage, all I can say is: Please post to this discussion if you come across any papers that used specfem and are not in the specfem google scholar profile. (Ideally, find a batch of 5 or so to post.) If you feel ambitious and want to comb the candidate papers, please do so! Having this list of papers is helpful for those authors and for current folks seeking to demonstrate the impact of specfem (such as for proposals). Thanks. |
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Please find some more specfem papers below that are not on the current list: Kaneko, Y., N. Lapusta, and J.-P. Ampuero (2008). Spectral element modeling of spontaneous earthquake rupture on rate and state faults: Effect of velocity-strengthening friction at shallow depths. Journal of Geophysical Research, 113, B09317, doi:10.1029/2007JB005553 Kaneko, Y. and N. Lapusta (2010). Supershear transition due to a free surface in 3-D simulations of spontaneous dynamic rupture on vertical strike-slip faults. Tectonophysics, 493(3-4), 272-284, doi:10.1016/j.tecto.2010.06.015 Konca, A.O., Y. Kaneko, N. Lapusta, and J.-P. Avouac (2013). Kinematic inversion of physically plausible earthquake source models obtained from dynamic rupture simulations. Bulletin of the Seismological Society of America, 103(5), 2621-2644, doi:10.1785/0120120358 Kaneko, Y. and P.M. Shearer (2014). Seismic source spectra and estimated stress drop derived from cohesive-zone models of circular subshear rupture. Geophysical Journal International, 197(2), 1002-1015, doi:10.1093/gji/ggu030 Kaneko, Y. and P.M. Shearer (2015). Variability of seismic source spectra, estimated stress drop and radiated energy, derived from cohesive-zone models of symmetrical and asymmetrical circular and elliptical ruptures. Journal of Geophysical Research, 120(2), 1053-1079, doi:10.1002/2014JB011642 Holden, C., Y. Kaneko, E. D'Anastasio, R. Benites, B. Fry, and I.J. Hamling (2017). The 2016 Kaikoura earthquake revealed by kinematic source inversion and seismic wavefield simulations: slow rupture propagation on a geometrically complex crustal fault network. Geophysical Research Letters, 44(22), 11320-11328, doi:10.1002/2017GL075301 Wallace, L.M., Y. Kaneko, S. Hreinsdottir, I.J. Hamling, Z. Peng, N. Bartlow, E. D'Anastasio, and B. Fry (2017). Large-scale dynamic triggering of shallow slow slip enhanced by overlying sedimentary wedge. Nature Geoscience, 10(10), 765-770, doi:10.1038/ngeo302 Warren-Smith, E., B. Fry, Y. Kaneko, and C.J. Chamberlain (2018). Foreshocks and delayed triggering of the 2016 MW7.1 Te Araroa earthquake and dynamic reinvigoration of its aftershock sequence by the MW7.8 Kaikoura earthquake, New Zealand. Earth and Planetary Science Letters, 482, 265-276, doi:10.1016/j.epsl.2017.11.020 Massey, C.I., D.B. Townsend, E. Rathje, K.E. Allstadt, B. Lukovic, Y. Kaneko, B. Bradley, J. Wartman, R.W. Jibson, D.M. Petley, N.A. Horspool, I.J. Hamling, J.M. Carey, S.C. Cox, J. Davidson, G.D. Dellow, G.W. Godt, C. Holden, K.E. Jones, A.E. Kaiser, M. Little, B.M. Lyndsell, S. McColl, R.M. Morgenstern, F.K. Rengers, D.A. Rhoades, B.J. Rosser, D.T. Strong, C. Singeisen, and M. Villeneuve (2018). Landslides triggered by the 14 November 2016 Mw 7.8 Kaikoura earthquake. New Zealand. Bulletin of the Seismological Society of America, 108(3B), 1630-1648, doi:10.1785/0120170305 McGuire, J.J., and Y. Kaneko (2018). Directly estimating earthquake rupture area using second moments to reduce the uncertainty in stress drop. Geophysical Journal International, 214(3), 2224–2235, doi:10.1093/gji/ggy201 Kearse, J., Y. Kaneko, T. Little, and R.J. Van Dissen (2019). Curved slickenlines preserve direction of rupture propagation. Geology, 47 (9): 838–842, doi:10.1130/G46563.1 Gusman, A.R., Y. Kaneko, W. Power, and D. Burbidge (2020). Source process for two enigmatic repeating vertical‐T CLVD tsunami earthquakes in the Kermadec Ridge. Geophysical Research Letters, 47 Yao, D., Z. Peng, Y. Kaneko, B. Fry, and X. Meng (2021). Dynamic triggering of earthquakes in the North Island of New Zealand following the 2016 Mw 7.8 Kaikōura earthquake. Earth and Planetary Science Letters, doi:10.1016/j.epsl.2020.116723 Howarth, J.D., A.R. Orpin, Y. Kaneko, et al. (2021). Calibrating the marine turbidite palaeoseismometer using the 2016 Kaikōura earthquake. Nature Geoscience, doi:10.1038/s41561-021-00692-6 Macklin, C., Y. Kaneko, and J. Kearse (2021). Coseismic slickenlines record the emergence of multiple rupture fronts during a surface-breaking earthquake. Tectonophysics, doi:10.1016/j.tecto.2021.228834 Inchin, P., J. Snively, Y. Kaneko, M. Zettergren, and A. Komjathy (2021). Inferring the evolution of a large earthquake from its acoustic impacts on the ionosphere. AGU Advances, doi:10.1029/2020AV000260 Inchin, P., J.A. Guerrero, J. Snively, and Y. Kaneko (2022). Simulation of infrasonic acoustic wave imprints on airglow layers during the 2016 M7.8 Kaikoura earthquake. Journal of Geophysical Research - Space Physics, doi:10.1029/2021JA029529 Kaneko, Y., and H. Goto (2022). The origin of large, long-period near-fault ground velocities during surface-breaking strike-slip earthquakes, Geophysical Research Letters, 49, e2022GL098029, doi:10.1029/2022GL098029 Gusman, A.R., J. Roger, W. Power, B. Fry, and Y. Kaneko (2022). The 2021 Loyalty Islands earthquake (Mw 7.7): Tsunami waveform inversion and implications for tsunami forecasting for New Zealand. Earth and Space Science, doi:10.1029/2022EA002346 Also, the following paper should be removed from the list as it wasn't using specfem: SM Day, LA Dalguer, N Lapusta, Y Liu, Journal of Geophysical Research: Solid Earth 110 (B12) Comparison of finite difference and boundary integral solutions to three‐dimensional spontaneous rupture, 2005 Thank you, |
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Added (and removed the 2005 Day article)! |
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How can one tell what the total number of papers is for a google scholar page (https://scholar.google.com/citations?user=bvjzHdUAAAAJ)? Can this be scraped, too, to display on the nice pubs page that @williameaton set up? Maybe it's too much, but we could have a "paper counter" and "citation counter" from the main page, similar to, say, the Alaska earthquake counter at the bottom of the AEC page (which is 39,140 for 2022, as of today, fyi). Of course, all this hinges on continually adding papers to the google scholar page. I still believe that human review is needed (and good for people to point out papers that need to be removed). Thanks. |
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The total publications is certainly doable. We already have "citations per year" on the Publications page but I'll add a "Total citations" to the main page over the weekend, though we may have to add the caveat that of course Google Scholar is not the most reliable tracker of citations... The citation count is harder, at least scraping the HTML from the outside-user perspective because it requires unrolling the whole page (clicking "Show more" at the bottom of the page...)...Im not sure if there is a way to trigger that automatically before pulling the HTML but others may know. It may be possible for the person who is logged into the account but I dont know if authentication issues will come up... Theres definitely some packages out there for scraping that I had not originally found, which may prove more fruitful for this stuff. |
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Thanks. The button-counters are blue skies. I do wonder why google scholar doesn't list the total number of papers in a profile; to me, this is more meaningful than (or at least comparably useful to) the total number of citations. Nothing urgent. |
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could be interesting? https://scholarly.readthedocs.io/en/stable/index.html
…On Fri, Nov 18, 2022 at 7:01 PM Carl Tape ***@***.***> wrote:
Thanks. The button-counters are blue skies. I do wonder why google scholar
doesn't list the total number of papers in a profile; to me, this is more
meaningful than (or at least comparably useful to) the total number of
citations. Nothing urgent.
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others about metamaterials
https://www.nature.com/articles/srep27717
https://www.nature.com/articles/srep19238
https://asa.scitation.org/doi/10.1121/1.4890942
https://www.nature.com/articles/srep25320
https://www.nature.com/articles/s41598-017-07151-6
On Fri, Nov 18, 2022 at 7:11 PM emanuele casarotti ***@***.***>
wrote:
… could be interesting?
https://scholarly.readthedocs.io/en/stable/index.html
On Fri, Nov 18, 2022 at 7:01 PM Carl Tape ***@***.***>
wrote:
> Thanks. The button-counters are blue skies. I do wonder why google
> scholar doesn't list the total number of papers in a profile; to me, this
> is more meaningful than (or at least comparably useful to) the total number
> of citations. Nothing urgent.
>
> —
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Thanks @casarotti for the suggestions with Scholarly...looks great and have implemented it in parts of the code. Not sure why it didnt come up before when searching for such tools! The next step with the publications is to have a list of seminal/theory papers covering the major developments of the SPECFEM code suites, e.g. Komatitsch and Vilotte 1998, Liu and Tromp 2006 etc etc... . These will likely be in the Training page of the website. These papers will be a static part of the website and I am happy to add them, but I don't think I am the best person to decide on which papers should be included. If anyone wants to take the lead on this, or give paper suggestions as a response to this comment that would be great! |
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I discover myself reading the long list of papers using specfem and finding
some hidden (for me) gems.
One thing that I would find useful is a tagging system (all the paper with
tag adjoint tomo for example)
it is an impossible work... I don't know if someone sees a quick way to do
that and also how to incorporate a "searchable database" in the static
website...
maybe the combo google scholars -> https://www.bibsonomy.org/ ->
https://github.com/rjoberon/bibsonomy-jekyll ?
but still it requires to tag manually the papers...
…On Tue, Nov 22, 2022 at 1:40 AM Will Eaton ***@***.***> wrote:
Thanks @casarotti <https://github.com/casarotti> for the suggestions with
Scholarly...looks great and have implemented it in parts of the code. Not
sure why it didnt come up before when searching for such tools!
The next step with the publications is to have a list of *seminal/theory
papers* covering the major developments of the SPECFEM code suites, e.g. *Komatitsch
and Vilotte 1998, Liu and Tromp 2006* etc etc... . These will likely be
in the Training page of the website.
These papers will be a static part of the website and I am happy to add
them, but I don't think I am the best person to decide on which papers
should be included. If anyone wants to take the lead on this, or give paper
suggestions as a response to this comment that would be great!
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@williameaton the foundational papers for earthquake dynamics with SPECFEM3D are: |
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Hi All. Two more SPECFEM papers (2D!) are
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Hi Jordan @jwbishop , |
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a new one
Simulations of Gravitoelastic Correlations for the Sardinian Candidate Site
of the Einstein Telescope
https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020JB020401
…On Mon, Nov 28, 2022 at 9:42 AM Jean Paul Ampuero ***@***.***> wrote:
Hi Jordan @jwbishop <https://github.com/jwbishop> ,
These two papers used the SEM2DPACK code (
https://github.com/jpampuero/sem2dpack), which is not part of the SPECFEM
suite; it branched out from the original version of Dimitri's 2D code
around 2000. Matt Haney and other colleagues trained at the Colorado School
of Mines often use SEM2PACK.
Cheers,
Pablo
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Added. |
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This article uses SPECFEM3D_CARTESIAN: |
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Added. |
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Here's a recent one that my automated google search found: 10.1190/geo2022-0027.1 |
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others |
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A recent paper on dynamic rupture simulation using SPECFEM3D: Aochi & Tsuda (2022) https://doi.org/10.1093/gji/ggac453 And one that used SPECFEM2D: Lior et al (2022) https://doi.org/10.1785/0220210349 |
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I established a google scholar profile for specfem here:
https://scholar.google.com/citations?user=bvjzHdUAAAAJ
I spent about 20 minutes "collecting" the papers that are currently there. My guess is that there are hundreds of specfem papers out there that are not in the profile. My suggestion is that some of us take a shift as "specfem publications lead". Brandon Vanderbeek offered to help next. (Thank you!)
The second item is that we need missing papers to be identified. I'm suggesting that people list the missing papers in this github discussion thread -- that way, the publications lead can locate them (in google scholar) and add them to the profile. And the publications lead can add them.
The main "quality control" is that we want to be sure that each paper is peer-reviewed and actually used specfem. (For example, probably not every single paper by Dmitry used specfem. Though reviewing all his publications would be worthwhile.)
If anyone notices a paper in the profile that did not use specfem or is not a journal paper, please post to this discussion and someone will remove it.
Eventually we might consider some level of categorization of the papers. But for now, I think it'd be a great achievement if we could identify the full set. This would give us some nice metrics to show the impact of specfem.
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