Merge branch 'debug' into encounter_storage

examples/Basic_Simulation/initial_conditions.py

@@ -11,24 +11,37 @@
 
 #!/usr/bin/env python3
 """
-Generates a set of Swiftest input files from initial conditions.
+Generates and runs a set of Swiftest input files from initial conditions with the SyMBA integrator. All simulation 
+outputs are stored in the /simdata subdirectory.
 
-Returns
--------
-Updates sim.data with the simulation data
+Input
+------
+None.
+
+Output
+------
+bin.nc         : A NetCDF file containing the simulation output.
+dump_bin1.nc   : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
+dump_bin2.nc   : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
+dump_param1.in : An ASCII file containing the necessary parameters to restart a simulation.
+dump_param2.in : An ASCII file containing the necessary parameters to restart a simulation.
+fraggle.log    : An ASCII file containing the information of any collisional events that occured.
+init_cond.nc   : A NetCDF file containing the initial conditions for the simulation.
+param.in       : An ASCII file containing the parameters for the simulation.
+swiftest.log   : An ASCII file containing the information on the status of the simulation as it runs.
 """
 
 import swiftest
 import numpy as np
 from numpy.random import default_rng
 
-# Initialize the simulation object as a variable
+# Initialize the simulation object as a variable. Arguments may be defined here or through the sim.run() method.
 sim = swiftest.Simulation(fragmentation=True, minimum_fragment_mass = 2.5e-11, mtiny=2.5e-8)
 
-# Add the modern planets and the Sun using the JPL Horizons Database
+# Add the modern planets and the Sun using the JPL Horizons Database.
 sim.add_solar_system_body(["Sun","Mercury","Venus","Earth","Mars","Jupiter","Saturn","Uranus","Neptune","Pluto"])
 
-# Add 5 user-defined massive bodies
+# Add 5 user-defined massive bodies.
 npl         = 5
 density_pl  = 3000.0 / (sim.param['MU2KG'] / sim.param['DU2M'] ** 3)
 
@@ -47,7 +60,7 @@
 
 sim.add_body(name=name_pl, a=a_pl, e=e_pl, inc=inc_pl, capom=capom_pl, omega=omega_pl, capm=capm_pl, Gmass=GM_pl, radius=R_pl, rhill=Rh_pl, Ip=Ip_pl, rot=rot_pl)
 
-# Add 10 user-defined test particles
+# Add 10 user-defined test particles.
 ntp = 10
 
 name_tp     = ["TestParticle_01", "TestParticle_02", "TestParticle_03", "TestParticle_04", "TestParticle_05", "TestParticle_06", "TestParticle_07", "TestParticle_08", "TestParticle_09", "TestParticle_10"]
@@ -59,8 +72,8 @@
 capm_tp     = default_rng().uniform(0.0, 360.0, ntp)
 
 sim.add_body(name=name_tp, a=a_tp, e=e_tp, inc=inc_tp, capom=capom_tp, omega=omega_tp, capm=capm_tp)
-# Display the run configuration parameters
+# Display the run configuration parameters.
 sim.get_parameter()
 
-# Run the simulation
+# Run the simulation. Arguments may be defined here or thorugh the swiftest.Simulation() method.
 sim.run(tstart=0.0, tstop=1.0e3, dt=0.01, tstep_out=1.0e0, dump_cadence=0)

examples/Basic_Simulation/output_reader.py

@@ -14,33 +14,32 @@
 Reads and processes a Swiftest output file.
 
 Input
--------
-out.nc     : NetCDF file
-    Swiftest output file.
+------
+bin.nc     : A NetCDF file containing the simulation output.
 
-Returns
--------
-output.eps : Encapsulated PostScript file.
-    A figure containing the eccentricity vs. semi-major axis for all bodies at the start of the simulation.
+Output
+------
+output.eps : Encapsulated PostScript file depicting the eccentricity vs. semi-major axis for all bodies at the start 
+             of the simulation.
 """
 
 import swiftest
 import xarray as xr
 import matplotlib.pyplot as plt
 
-# Read in the simulation output and store it as an Xarray dataset
-ds = swiftest.Simulation(param_file="simdata/param.in", read_old_output_file=True).data
+# Read in the simulation output and store it as an Xarray dataset.
+sim = swiftest.Simulation(read_old_output_file=True)
 
-# Plot of the data and save the output plot
-colors = ['white' if x == 'Massive Body' else 'black' for x in ds['particle_type']]
-sizes = [100 if x == 'Massive Body' else 10 for x in ds['particle_type']]
+# Plot of the data and save the output plot.
+colors = ['white' if x == 'Massive Body' else 'black' for x in sim.data['particle_type']]
+sizes = [100 if x == 'Massive Body' else 10 for x in sim.data['particle_type']]
 
 fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(5,3))
-ax.set(xlabel="Semimajor Axis (AU)", ylabel="Eccentricity", title="Simulation Start")
-ax.scatter(ds['a'].isel(time=0), ds['e'].isel(time=0), c=colors, s=sizes, edgecolor='black')
+ax.set(xlabel="Semimajor Axis (AU)", ylabel="Eccentricity", title="Simulation Initial Conditions (t=0)")
+ax.scatter(sim.data['a'].isel(time=0), sim.data['e'].isel(time=0), c=colors, s=sizes, edgecolor='black')
 ax.set_xlim(0, 2.0)
 ax.set_ylim(0, 0.4)
-ax.text(1.5, 0.35, f"t = {ds['time'].isel(time=0).values} years", size=10, ha="left")
+ax.text(1.5, 0.35, f"t = {sim.data['time'].isel(time=0).values} years", size=10, ha="left")
 plt.tight_layout()
 plt.show()
-fig.savefig("output.eps", dpi=300, facecolor='white', transparent=False, bbox_inches="tight")
+fig.savefig("output.eps", dpi=300, facecolor='white', transparent=False, bbox_inches="tight")