Added readme.md to Getting Started Guide

docs/getting-started-guide/index.rst

@@ -12,6 +12,7 @@ Carlisle Wishard, David Minton, Jennifer Pouplin, Jake Elliott, & Dana Singh
 
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+
 Swiftest is a software packaged designed to model the dynamical
 evolution of gravitational systems. Swiftest is an extension of the
 `Swifter <https://www.boulder.swri.edu/swifter/>`__ software package,
@@ -64,8 +65,8 @@ will install a standalone executable called ``swiftest_driver``, which
 can execute simulations from the command line, provided that initial
 conditions and configuration files are available in the path.
 
-**Building the ``swiftest`` Python package and standalone
-``swiftest_driver`` executable**
+**Building the** ``swiftest`` **Python package and standalone**
+``swiftest_driver`` **executable**
 
 Swiftest is designed to be downloaded, compiled, and run on a Linux or
 MacOS based system. Windows support is currently being developed.
@@ -143,7 +144,7 @@ compile, edit, and run as you see fit.
 
 **Compiling the Swiftest driver program**
 
-**Compiling ``swiftest_driver`` using Docker**
+**Compiling** ``swiftest_driver`` **using Docker**
 
 By far the simplest, most reliable way of compiling the driver program
 is via a Docker container. The Swiftest project contains a Dockerfile
@@ -180,14 +181,14 @@ in the ``bin/`` directory.
 The optional Docker argument ``EXTRA_CMAKE_OPTIONS`` is provided to pass
 any additional CMake arguments (see below).
 
-**Compiling ``swiftest_driver`` using CMake** Several build scripts are
+**Compiling** ``swiftest_driver`` **using CMake** Several build scripts are
 available in the ``buildscripts`` folder for building Swiftest and its
 dependencies on a Linux or Mac system. These are used when generating
 the official Swiftest Python wheels using cibuildwheel. To build the
 complete project, run ``buildscripts\build_all.sh`` from the command
 line.
 
-**Compiling ``swiftest_driver`` using CMake**
+**Compiling** ``swiftest_driver`` **using CMake**
 
 The Swiftest driver program is written in modern Fortran and must be
 compiled before it can be run. After compilation, an executable, called
@@ -612,11 +613,13 @@ Where ``INTEGRATOR`` is your integrator of choice, either ``whm``,
 
 The number and type of output files generated by Swiftest depends on the
 input parameters selected and the method through which Swiftest was run.
-The standard output files are as follows: - **data.nc** - Always
+The standard output files are as follows: 
+- **data.nc** - Always
 generated, the output file containing the information for every body in
 the system, recorded every ``ISTEP_OUT`` timesteps and written every
 ``DUMP_CADENCE``. This file can be analyzed using the Swiftest Python
-package (``sim.data``). - **collisions.log** - The log containing the
+package (``sim.data``). 
+- **collisions.log** - The log containing the
 record of each fragmentation event, including the collisional regime,
 and the number of the fragments created, only if ``FRAGMENTATION`` is
 ``YES``, Swiftest SyMBA only. - **swiftest.log** - A log containing a
@@ -750,7 +753,7 @@ output file, is as follows:
 
    Fraggle logfile
 
-     **********************************************************************************************************************
+    ***********************************************************************************************************************
     Collision between massive bodies detected at time t = 2.063709800335315E-006
     **********************************************************************************************************************
 
@@ -1199,7 +1202,9 @@ References
 -  Wisdom, J. and Holman, M. (1991). Symplectic maps for the N-body
    problem. **The Astronomical Journal**, 102. `doi:
    0.1086/115978 <https://ui.adsabs.harvard.edu/abs/1991AJ....102.1528W/abstract>`__
--  Wishard et al. (2023) - In preparation
+-  Wishard et al. (2023) - Swiftest: An *N*-body Integrator for 
+   Gravitational Systems. **Journal of Open Source Software**, 8(90), 5409, 
+   `https://doi.org/10.21105/joss.05409 <https://doi.org/10.21105/joss.05409>`__
 
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