Merge branch 'debug' of github.itap.purdue.edu:MintonGroup/swiftest i…

…nto debug

examples/.gitignore

@@ -5,4 +5,5 @@
 !helio_gr_test
 !whm_gr_test
 !Chambers2013
-!solar_impact
+!solar_impact
+!Swifter_Swiftest

examples/Basic_Simulation/.gitignore

@@ -2,5 +2,4 @@
 !.gitignore
 !initial_conditions.py
 !output_reader.py
-!run_from_file.py
-!read_old_run.py
+!README.txt

examples/Basic_Simulation/README.txt

@@ -0,0 +1,23 @@
+Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+This file is part of Swiftest.
+Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with Swiftest. 
+If not, see: https://www.gnu.org/licenses. 
+
+README.txt
+
+Swiftest Example : Basic_Simulation
+Author           : Carlisle Wishard and David Minton
+Date             : December 6, 2022
+
+Included in the Basic_Simulation example directory are the following files:
+
+	- README.txt            : This file
+	- initial_conditions.py : A Python Script that generates and runs a set of initial conditions.
+	- output_reader.py      : A Python Script that processes out.nc and generates output.eps
+
+This example is intended to be run with Swiftest SyMBA. For details on how to generate, run, and analyze this example, 
+see the Swiftest User Manual.

examples/Basic_Simulation/initial_conditions.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
  Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
  This file is part of Swiftest.
@@ -9,7 +11,6 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-#!/usr/bin/env python3
 """
 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.
@@ -20,12 +21,8 @@
 
 Output
 ------
-data.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.
+data.nc        : A NetCDF file containing the simulation output.
+collisions.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.

examples/Basic_Simulation/output_reader.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
  Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
  This file is part of Swiftest.
@@ -9,7 +11,6 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-#!/usr/bin/env python3
 """
 Reads and processes a Swiftest output file.
 

examples/Chambers2013/.gitignore

@@ -1,4 +1,5 @@
 *
 !.gitignore
 !init_cond.py
-!scattermovie.py
+!scattermovie.py
+!README.txt

examples/Chambers2013/README.txt

@@ -0,0 +1,23 @@
+Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+This file is part of Swiftest.
+Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with Swiftest. 
+If not, see: https://www.gnu.org/licenses. 
+
+README.txt
+
+Swiftest Example : Chambers2013
+Author           : David Minton and Carlisle Wishard
+Date             : December 6, 2022
+
+Included in the Chambers2013 example directory are the following files:
+
+	- README.txt      : This file
+	- init_cond.py    : A Python Script that generates and runs a set of initial conditions.
+	- scattermovie.py : A Python Script that processes data.nc and generates Chambers2013-aescatter.mp4 or Chambers2013-aiscatter.mp4
+
+This example is intended to be run with Swiftest SyMBA. For details on how to generate, run, and analyze this example, 
+see the Swiftest User Manual.

examples/Chambers2013/init_cond.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
  Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
  This file is part of Swiftest.
@@ -9,7 +11,20 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-#!/usr/bin/env python3
+"""
+Generates a set of Swiftest input files from initial conditions with the SyMBA integrator. All simulation 
+outputs are stored in the /simdata subdirectory.
+
+Input
+------
+None.
+
+Output
+------
+init_cond.nc   : A NetCDF file containing the initial conditions for the simulation.
+param.in       : An ASCII file containing the parameters for the simulation.
+"""
+
 import swiftest
 import numpy as np
 from numpy.random import default_rng

examples/Chambers2013/scattermovie.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
  Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
  This file is part of Swiftest.
@@ -9,7 +11,22 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-#!/usr/bin/env python3
+"""
+Creates a movie from a set of Swiftest output files. All simulation 
+outputs are stored in the /simdata subdirectory.
+
+Input
+------
+param.in    : ASCII Swiftest parameter input file.
+data.nc     : A NetCDF file containing the simulation output.
+
+Output
+------
+Chambers2013-aescatter.mp4  : A .mp4 file plotting eccentricity vs semimajor axis. 
+OR 
+Chambers2013-aiscatter.mp4  : A .mp4 file plotting inclination vs semimajor axis. 
+"""
+
 import swiftest 
 import numpy as np
 import matplotlib.pyplot as plt

examples/Fragmentation/.gitignore

@@ -2,3 +2,5 @@
 !.gitignore
 !Fragmentation_Movie.py
 !Multibody_Movie.py
+!swiftest_fragmentation.py
+!README.txt

examples/Fragmentation/Fragmentation_Movie.py

@@ -15,15 +15,12 @@
 
 Inputs
 _______
-param.in : ASCII text file
-    Swiftest parameter input file.
-out.nc   : NetCDF file
-    Swiftest output file.
+param.in    : ASCII Swiftest parameter input file.
+data.nc     : A NetCDF file containing the simulation output.
 
 Returns
 -------
-fragmentation.mp4 : mp4 movie file
-    Movie of a fragmentation event.
+fragmentation.mp4 : A .mp4 file of a fragmentation event.
 """
 
 import swiftest

examples/Fragmentation/Multibody_Movie.py

@@ -15,15 +15,12 @@
 
 Inputs
 _______
-param.in : ASCII text file
-    Swiftest parameter input file.
-out.nc   : NetCDF file
-    Swiftest output file.
+param.in    : ASCII Swiftest parameter input file.
+data.nc     : A NetCDF file containing the simulation output.
 
 Returns
 -------
-fragmentation.mp4 : mp4 movie file
-    Movie of a fragmentation event.
+fragmentation.mp4 : A .mp4 file of a fragmentation event.
 """
 
 import swiftest

examples/Fragmentation/README.txt

@@ -0,0 +1,23 @@
+Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+This file is part of Swiftest.
+Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with Swiftest. 
+If not, see: https://www.gnu.org/licenses. 
+
+README.txt
+
+Swiftest Example : Fragmentation
+Author           : David Minton and Carlisle Wishard
+Date             : December 6, 2022
+
+Included in the Fragmentation example directory are the following files:
+
+	- README.txt 		    : This file
+	- swiftest_fragmentation.py : A Python Script that generates and runs three sets of initial conditions.
+	- Fragmentation_Movie.py    : A Python Script that processes an out.nc file and generates a movie (.mp4) of a collisional event.
+	- Multibody_Movie.py        : A Python Script that processes an out.nc file and generates a movie (.mp4) of a multi-body collisional event.
+
+This example is intendedto be run with Swiftest SyMBA. For details on how to generate, run, and analyze this example, see the Swiftest User Manual.

examples/Fragmentation/swiftest_fragmentation.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
  Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
  This file is part of Swiftest.
@@ -8,7 +10,7 @@
  You should have received a copy of the GNU General Public License along with Swiftest.
  If not, see: https://www.gnu.org/licenses.
 """
-#!/usr/bin/env python3
+
 """
 Generates and runs a set of Swiftest input files from initial conditions with the SyMBA integrator. All simulation 
 outputs for the disruption case are stored in the /disruption subdirectory. All simulation outputs for the hit and run 
@@ -31,11 +33,7 @@
 init_cond.nc        : A NetCDF file containing the initial conditions for the simulation.
 collision_000001.nc : A NetCDF file containing the data for the collisions.
 encounter_000001.nc : A NetCDF file containing the data for the close encounters.
-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.
+collisions.log      : An ASCII file containing the information of any collisional events that occured.
 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.
 

examples/Swifter_Swiftest/.gitignore

@@ -0,0 +1,4 @@
+*
+!.gitignore
+!8pl_0tp
+!108_pl_50tp

examples/Swifter_Swiftest/8pl_0tp/.gitignore

@@ -0,0 +1,12 @@
+*
+!.gitignore
+!cb.swiftest.in
+!init_cond.py
+!param.swifter.in
+!param.swiftest.in
+!pl.swifter.in
+!pl.swiftest.in
+!README.txt
+!tp.swifter.in
+!tp.swiftest.in
+!swiftest_symba_vs_swifter_symba.ipynb

examples/Swifter_Swiftest/8pl_0tp/README.txt

@@ -0,0 +1,29 @@
+Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+This file is part of Swiftest.
+Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+You should have received a copy of the GNU General Public License along with Swiftest. 
+If not, see: https://www.gnu.org/licenses. 
+
+README.txt
+
+Swiftest Example : Swifter_Swiftest/8pl_0tp
+Author           : David Minton and Carlisle Wishard
+Date             : August 15, 2022
+
+Included in the symba_swifter_comparison/8pl example directory are the following files:
+
+	- README.txt                            : This file
+	- param.swiftest.in                     : The Swiftest parameter input file
+	- param.swifter.in                      : The Swifter parameter input file
+	- cb.swiftest.in                        : The Swiftest central body input file
+	- pl.swifter.in                         : The Swifter massive body input file
+	- pl.swiftest.in                        : The Swiftest massive body input file
+	- tp.swifter.in                         : The Swifter test particle input file
+	- tp.swiftest.in                        : The Swiftest test particle input file
+	- init_cond.py                          : A Python Script that generates two sets of initial conditions: one Swifter and one Swiftest
+	- swiftest_symba_vs_swifter_symba.ipynb : A Jupyter Notebook for processing and analysing Swifter and Swiftest data
+
+This example is intended to be run with the SyMBA integrator for both Swifter and Swiftest. For details on how to generate, run, and analyze this example, see the Swiftest User Manual. To obtain a copy of Swifter, please see https://www.boulder.swri.edu/swifter/home.html.

examples/symba_swifter_comparison/8pl/init_cond.py → examples/Swifter_Swiftest/8pl_0tp/init_cond.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 """
  Copyright 2023 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
  This file is part of Swiftest.
@@ -9,7 +11,26 @@
  If not, see: https://www.gnu.org/licenses. 
 """
 
-#!/usr/bin/env python3
+"""
+Generates and runs a set of Swiftest input files and a set of Swifter input files from initial conditions with the 
+SyMBA integrator. 
+
+Input
+------
+None.
+
+Output
+------
+param.swiftest.in      : An ASCII file containing the parameters for the Swiftest simulation.
+param.swifter.in       : An ASCII file containing the parameters for the Swifter simulation.
+cb.swiftest.in         : An ASCII file containing the central body data for the Swiftest simulation.
+pl.swifter.in          : An ASCII file containing the massive body data for the Swifter simulation.
+pl.swiftest.in         : An ASCII file containing the massive body data for the Swiftest simulation.
+tp.swifter.in          : An ASCII file containing the test particle data for the Swifter simulation.
+tp.swiftest.in         : An ASCII file containing the test particle data for the Swiftest simulation.
+
+"""
+
 import numpy as np
 import swiftest
 import swiftest.io as swio