From ecd3755a412921fe586958e19fd6c5d37288b785 Mon Sep 17 00:00:00 2001 From: bonachea Date: Fri, 7 Feb 2025 16:51:13 -0500 Subject: [PATCH] Fix citations, strip out fake citations, minor editing Brad decided to use LBNL as his affiliation --- docs/joss/paper.bib | 11 ++++++++++- docs/joss/paper.md | 23 +++++++++-------------- 2 files changed, 19 insertions(+), 15 deletions(-) diff --git a/docs/joss/paper.bib b/docs/joss/paper.bib index e20d9601c..0ce9c4add 100644 --- a/docs/joss/paper.bib +++ b/docs/joss/paper.bib @@ -1,5 +1,5 @@ @inproceedings{rouson2022caffeine, - title={Caffeine: Coarray Fortran framework of efficient interfaces to network environments}, + title = {{Caffeine: CoArray Fortran Framework of Efficient Interfaces to Network Environments}}, author={Rouson, Damian and Bonachea, Dan}, booktitle={2022 IEEE/ACM Eighth Workshop on the LLVM Compiler Infrastructure in HPC (LLVM-HPC)}, pages={34--42}, @@ -69,10 +69,19 @@ @misc{caffeine-site title = {{Caffeine: CoArray Fortran Framework of Efficient Interfaces to Network Environments}}, publisher = {GitHub}, journal = {GitHub repository}, + year = 2025, note = "\url{https://go.lbl.gov/caffeine}", url = {https://github.com/berkeleylab/caffeine} } +@misc{class-site, + author={{Lawrence Berkeley National Laboratory}}, + title = {{iComputer Languages & Systems Software Group}}, + journal = {Web page}, + year = 2025, + url = {https://go.lbl.gov/class} +} + # -------------------------------------------------------------------------- @book{fortran2023, diff --git a/docs/joss/paper.md b/docs/joss/paper.md index 8ce70959b..244cd9e98 100644 --- a/docs/joss/paper.md +++ b/docs/joss/paper.md @@ -18,7 +18,7 @@ authors: - name: Brad Richardson orcid: 0000-0002-3205-2169 equal-contrib: true - affiliation: 2 + affiliation: 1 - name: Damian Rouson orcid: 0000-0002-2344-868X equal-contrib: true @@ -26,8 +26,6 @@ authors: affiliations: - name: Lawrence Berkeley National Laboratory, United States index: 1 - - name: Amentum Services, Inc., United States - index: 2 date: 5 February 2025 bibliography: paper.bib @@ -40,7 +38,7 @@ single-program, multiple-data (SPMD) parallel programming and loop parallelism beginning with [@fortran2008]. The SPMD features involve the creation of a fixed number of images (instances) of a program that execute asynchronously in shared or distributed memory except where -a programmer except where a programmer explicitly imposes synchronization. +a programmer explicitly imposes synchronization. Coarrays employ a subscripted multidimensional array notation to define a partitioned global address space (PGAS) that images can use to communicate data with each other. The CoArray Fortran Framework of Efficient Interfaces @@ -64,17 +62,16 @@ Cython-optimized) implementations of common operations such as gravitational potential and force evaluation, orbit integration, dynamical transformations, and chaos indicators for nonlinear dynamics. `Gala` also relies heavily on and interfaces well with the implementations of physical units and astronomical -coordinate systems in the `Astropy` package [@astropy] (`astropy.units` and -`astropy.coordinates`). +coordinate systems in the `Astropy` package `Gala` was designed to be used by both astronomical researchers and by students in courses on gravitational dynamics or astronomy. It has already been -used in a number of scientific publications [@Pearson:2017] and has also been +used in a number of scientific publications and has also been used in graduate courses on Galactic dynamics to, e.g., provide interactive -visualizations of textbook material [@Binney:2008]. The combination of speed, +visualizations of textbook material . The combination of speed, design, and support for Astropy functionality in `Gala` will enable exciting scientific explorations of forthcoming data releases from the *Gaia* mission -[@gaia] by students and experts alike. +by students and experts alike. # Mathematics @@ -99,9 +96,6 @@ Citations to entries in paper.bib should be in [rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) format. -If you want to cite a software repository URL (e.g. something on GitHub without a preferred -citation) then you can do it with the example BibTeX entry below for @fidgit. - For a quick reference, the following citation commands can be used: - `@author:2001` -> "Author et al. (2001)" - `[@author:2001]` -> "(Author et al., 2001)" @@ -122,12 +116,13 @@ Test citations: # Figures -Figures \autoref{fig:example} depicts a Fortran software stack in which a parallel runtime library such as Caffeine supportes compiled Fortran code by implementing PRIF. +Figures \autoref{fig:prif-stack} depicts a Fortran software stack in which a parallel runtime library such as Caffeine supportes compiled Fortran code by implementing PRIF. ![The parallel Fortran software stack enabled by the Caffeine parallel runtime PRIF implementation.\label{fig:prif-stack}](PRIF-software-stack-with-more.pdf){ width=100% } # Acknowledgements -The Computer Languages and Systems Software (CLaSS) Group at Berkeley Lab has developed Caffeine development on funding from the Exascale Computing Project (ECP) and the Stewardship for Programming Systems and Tools (S4PST) project. +The Computer Languages and Systems Software (CLaSS) Group at Berkeley Lab [@class-site] +has developed Caffeine on funding from the Exascale Computing Project (ECP) and the Stewardship for Programming Systems and Tools (S4PST) project. # References