Merge pull request #28 from profminton/master

Updated the paper
MintonGroup · Oct 7, 2023 · 931fa88 · 931fa88
2 parents b284298 + 30737f6
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diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
diff --git a/.gitignore b/.gitignore
@@ -19,7 +19,7 @@ swiftest_driver.sh
 !README.swifter 
 dump*
 !**/.gitignore
-!.github/workflows/build_wheels.yml
+!.github/workflows/*.yml
 !setup.py
 !examples/**
 !swiftest/**

diff --git a/cmake/Modules/SetSwiftestFlags.cmake b/cmake/Modules/SetSwiftestFlags.cmake
@@ -564,8 +564,10 @@ IF (CMAKE_BUILD_TYPE STREQUAL "RELEASE" OR CMAKE_BUILD_TYPE STREQUAL "PROFILE")
             )
             # Tells the compiler to link to certain libraries in the Intel oneAPI Math Kernel Library (oneMKL). 
             SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
-                Fortran "-qmkl=cluster" # Intel
-                        "-qmkl"     # Intel
+                Fortran "-mkl=cluster" 
+                        "-mkl"
+                        "-qmkl=cluster"
+                        "-qmkl"     
             ) 
             # Enables additional interprocedural optimizations for a single file compilation
             SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE}"
@@ -614,7 +616,7 @@ IF (COMPILER_OPTIONS STREQUAL "Intel")
     ELSE ()
         # Some subroutines require more strict floating point operation optimizations for repeatability
         SET_COMPILE_FLAG(STRICTMATH_FLAGS "${STRICTMATH_FLAGS}"
-            Fortran "-fp-module=precise" # Intel 
+            Fortran "-fp-model=precise" # Intel 
         )
         SET_COMPILE_FLAG(STRICTMATH_FLAGS "${STRICTMATH_FLAGS}"
             Fortran "-prec-div" # Intel 

diff --git a/paper/paper.bib b/paper/paper.bib
@@ -1,3 +1,69 @@
+@article{Chambers:1999,
+	title = {A hybrid symplectic integrator that permits close encounters between massive bodies},
+	volume = {304},
+	url = {http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1999MNRAS.304..793C&link_type=ABSTRACT},
+	doi = {10.1046/j.1365-8711.1999.02379.x},
+	number = {4},
+	author = {Chambers, J E},
+	month = apr,
+	year = {1999},
+	pages = {793--799},
+}
+
+@article{Duncan:1998,
+	title = {A {Multiple} {Time} {Step} {Symplectic} {Algorithm} for {Integrating} {Close} {Encounters}},
+	volume = {116},
+	url = {http://stacks.iop.org/1538-3881/116/i=4/a=2067},
+	doi = {10.1086/300541},
+	number = {4},
+	journal = {The Astronomical Journal},
+	author = {Duncan, Martin J and Levison, Harold F and Lee, Man Hoi},
+	month = oct,
+	year = {1998},
+	pages = {2067--2077},
+}
+
+
+@article{Grimm:2022,
+	title = {{GENGA}. {II}. {GPU} {Planetary} {N}-body {Simulations} with {Non}-{Newtonian} {Forces} and {High} {Number} of {Particles}},
+	volume = {932},
+	issn = {0004-637X},
+	url = {https://dx.doi.org/10.3847/1538-4357/ac6dd2},
+	doi = {10.3847/1538-4357/ac6dd2},
+	language = {en},
+	number = {2},
+	urldate = {2023-10-06},
+	journal = {The Astrophysical Journal},
+	author = {Grimm, Simon L. and Stadel, Joachim G. and Brasser, Ramon and Meier, Matthias M. M. and Mordasini, Christoph},
+	month = jun,
+	year = {2022},
+	pages = {124},
+}
+
+
+@misc{kaufmann_swifter_nodate,
+	title = {Swifter},
+	url = {https://www.boulder.swri.edu/swifter/},
+	abstract = {The Swifter software package, written by David E. Kaufmann, is a completely redesigned and improved version of the Swift package of Hal Levison and Martin Duncan. Like Swift, Swifter is designed to integrate a set of mutually gravitationally interacting bodies together with a group of massless test particles that feel the gravitational influence of the massive bodies but do not affect each other or the massive bodies. In addition, the SyMBA integrator supports a second class of massive bodies whose masses are less than some user-specified value. These bodies gravitationally interact with the more massive bodies, but do not interact with each other. Seven integration techniques are included in the current beta release of Swifter:},
+	urldate = {2023-10-06},
+	journal = {Swifter — an improved solar system integration software package},
+	author = {Kaufmann, David E.},
+}
+
+@article{Leinhardt:2012,
+	title = {Collisions between {Gravity}-dominated {Bodies}. {I}. {Outcome} {Regimes} and {Scaling} {Laws}},
+	volume = {745},
+	url = {http://stacks.iop.org/0004-637X/745/i=1/a=79},
+	doi = {10.1088/0004-637X/745/1/79},
+	number = {1},
+	journal = {The Astrophysical Journal},
+	author = {Leinhardt, Zoë M and Stewart, Sarah T},
+	month = jan,
+	year = {2012},
+	pages = {79},
+}
+
+
 @article{Levison:1994,
   	Author = {{Levison}, H. and {Duncan}, M.},
   	Journal = {Icarus},
@@ -9,24 +75,120 @@ @article{Levison:1994
    url = {https://www.sciencedirect.com/science/article/pii/S0019103584710396?via%3Dihub}
 }
 
-@article{Duncan:1998,
-  	Author = {{Duncan}, M., {Levison}, H., and {Lee}, M. H.},
-  	Journal = {The Astronomical Journal},
-  	Title = {{A Multiple Time Step Symplectic Algorithm for Integrating Close Encounters}},
-  	Year = 1998, 
-   Month = oct, 
-   Volume = 116, 
-   DOI =  {10.1086/300541},
-   url = {https://iopscience.iop.org/article/10.1086/300541}
+
+@article{Levison:2000,
+	title = {Symplectically {Integrating} {Close} {Encounters} with the {Sun}},
+	volume = {120},
+	issn = {0004-6256},
+	url = {http://dx.doi.org/10.1086/301553},
+	doi = {10.1086/301553},
+	number = {4},
+	journal = {The Astronomical Journal},
+	author = {Levison, Harold F. and Duncan, Martin J.},
+	month = oct,
+	year = {2000},
+	pages = {2117--2123},
 }
 
-@article{Leinhardt:2012,
-  	Author = {{Leinhardt}, Z. and {Stewart}, S.},
-  	Journal = {The Astronomical Journal},
-  	Title = {{Collisions between Gravity-dominated Bodies. I. Outcome Regimes and Scaling Laws.}},
-  	Year = 2012, 
-   Month = dec, 
-   Volume = 745, 
-   DOI =  {10.1088/0004-637X/745/1/79},
-   url = {https://iopscience.iop.org/article/10.1088/0004-637X/745/1/79}
+@article{Moore:2011,
+	title = {{QYMSYM}: {A} {GPU}-accelerated hybrid symplectic integrator that permits close encounters},
+	volume = {16},
+	url = {http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=2011NewA...16..445M&link_type=ABSTRACT},
+	doi = {10.1016/j.newast.2011.03.009},
+	number = {7},
+	journal = {New Astronomy},
+	author = {Moore, Alexander and Quillen, Alice C},
+	month = nov,
+	year = {2011},
+	pages = {445--455},
+}
+
+@article{Rein:2012,
+	title = {{REBOUND}: an open-source multi-purpose {N}-body code for collisional dynamics},
+	volume = {537},
+	url = {http://www.aanda.org/10.1051/0004-6361/201118085},
+	doi = {10.1051/0004-6361/201118085},
+	journal = {Astronomy \& Astrophysics},
+	author = {Rein, H and Liu, S F},
+	month = jan,
+	year = {2012},
+	pages = {A128},
+}
+
+
+@article{Rein:2015,
+	title = {`whfast`': a fast and unbiased implementation of a symplectic {Wisdom}–{Holman} integrator for long-term gravitational simulations},
+	volume = {452},
+	issn = {0035-8711},
+	shorttitle = {whfast},
+	url = {https://doi.org/10.1093/mnras/stv1257},
+	doi = {10.1093/mnras/stv1257},
+	number = {1},
+	urldate = {2023-10-06},
+	journal = {Monthly Notices of the Royal Astronomical Society},
+	author = {Rein, Hanno and Tamayo, Daniel},
+	month = sep,
+	year = {2015},
+	pages = {376--388},
+}
+
+
+@article{Rein:2019,
+	title = {Hybrid symplectic integrators for planetary dynamics},
+	volume = {485},
+	issn = {0035-8711},
+	url = {https://academic.oup.com/mnras/article/485/4/5490/5380811},
+	doi = {10.1093/mnras/stz769},
+	number = {4},
+	journal = {Monthly Notices of the Royal Astronomical Society},
+	author = {Rein, Hanno and Hernandez, David M. and Tamayo, Daniel and Brown, Garett and Eckels, Emily and Holmes, Emma and Lau, Michelle and Leblanc, Réjean and Silburt, Ari},
+	month = jun,
+	year = {2019},
+	pages = {5490--5497},
+}
+
+@misc{rein_welcome_nodate,
+	title = {Welcome to {REBOUND} - {REBOUND}},
+	url = {https://rebound.readthedocs.io/en/latest/},
+	urldate = {2023-10-06},
+	journal = {Welcome to REBOUND - REBOUND},
+	author = {Rein, Hanno},
+}
+
+@article{Saha:1994,
+	title = {Long-term planetary integration with individual time steps},
+	volume = {108},
+	url = {http://adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1994AJ....108.1962S&link_type=ABSTRACT},
+	doi = {10.1086/117210},
+	journal = {The Astronomical Journal},
+	author = {Saha, Prasenjit and Tremaine, Scott},
+	month = nov,
+	year = {1994},
+	pages = {1962--1969},
+}
+
+@article{Stewart:2012,
+	title = {Collisions between {Gravity}-dominated {Bodies}. {II}. {The} {Diversity} of {Impact} {Outcomes} during the {End} {Stage} of {Planet} {Formation}},
+	volume = {751},
+	url = {http://stacks.iop.org/0004-637X/751/i=1/a=32},
+	doi = {10.1088/0004-637X/751/1/32},
+	number = {1},
+	journal = {The Astrophysical Journal},
+	author = {Stewart, Sarah T and Leinhardt, Zoë M},
+	month = jan,
+	year = {2012},
+	pages = {32},
+}
+
+
+@article{Wisdom:1991,
+	title = {Symplectic maps for the n-body problem},
+	volume = {102},
+	url = {http://adsabs.harvard.edu/cgi-bin/bib_query?1991AJ....102.1528W},
+	doi = {10.1086/115978},
+	journal = {The Astronomical Journal},
+	author = {Wisdom, Jack and Holman, Matthew},
+	month = oct,
+	year = {1991},
+	pages = {1528--1538},
 }