Cleaned up the basic simulation example page a bit

docs/user-guide/basic-simulation/index.rst

@@ -12,13 +12,14 @@ Start with importing Swiftest. ::
 Initial Simulation Setup 
 ===========================
 
-Create a Swiftest Simulation object.
+Create a Swiftest :class:`Simulation <swiftest.Simulation>` object.
 Outputs are stored in the ``./simdata`` directory by default. ::
 
    sim = swiftest.Simulation()
 
 Now that we have a simulation object set up (with default parameters), we can add bodies to the simulation. 
-The biggest body in the simulation is taken as the central body.
+The biggest body in the simulation is taken as the central body. Swiftest sets a Simulation object up with a set of default parameters, 
+including a default unit system of AU, y, and solar masses.
 
 Solar System Bodies
 =========================
@@ -40,16 +41,39 @@ Add other small bodies too: ::
 Running the Simulation
 ========================
 
-We now set up the simulation parameters. Here we have a simulation starting from `0.0 y` and running for `1 My = 1e6 years` 
-with time steps of `0.01 years`. ::
+We now can some simulation parameters using the :func:`set_parameter <swiftest.Simulation.set_parameter>` method. 
+Here we have a simulation that runs for 1 My a step size of 0.01 y. We will also save the system every 1000 y and wait until the end of the simulation to write the simulation data to file using the ``dump_cadence=0`` argument ::
 
-    sim.set_parameter(tstart=0.0, tstop=1.0e6, dt=0.01)
+    sim.set_parameter(tstop=1.0e6, tstep_out=1e3, dt=0.01, dump_cadence=0)
 
-Once everything is set up, we can save the simulation object and then run it: ::
+Once everything is set up, we call the :func:`run <swiftest.Simulation.run>` method to integrate the system forward in time::
 
-    sim.save()
     sim.run()
 
+Swiftest is relatively flexible with arguments. You can pass the parameters in when initializing the simulation object, or even later when running.
+So the following are all equivalent::
+
+    sim = swiftest.Simulation(tstop=1.0e6, tstep_out=1e3, dt=0.01, dump_cadence=0)
+    sim.add_solar_system_body(["Sun","Mercury","Venus","Earth","Mars","Jupiter","Saturn","Uranus","Neptune"])
+    sim.run()
+
+    sim = swiftest.Simulation()
+    sim.add_solar_system_body(["Sun","Mercury","Venus","Earth","Mars","Jupiter","Saturn","Uranus","Neptune"])
+    sim.set_parameter(tstop=1.0e6, tstep_out=1e3, dt=0.01, dump_cadence=0)
+    sim.run()
+
+    sim = swiftest.Simulation()
+    sim.add_solar_system_body(["Sun","Mercury","Venus","Earth","Mars","Jupiter","Saturn","Uranus","Neptune"])
+    sim.run(tstop=1.0e6, tstep_out=1e3, dt=0.01, dump_cadence=0)
+
+
+Analayzing Simulation Output
+=============================
+
+Once a simulation has been run, its output data is stored in the ``./simdata`` directory. The main data is stored in a file with a 
+default name of ``data.nc``, which is a netCDF file. It is read in and stored as an `Xarray Dataset <https://docs.xarray.dev/en/stable/>`__ object in the ``sim.data`` attribute.
+
+
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