Merge branch 'debug'

MintonGroup · Feb 7, 2023 · c6c2989 · c6c2989
2 parents f5cb6b9 + d9394d5
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diff --git a/examples/Basic_Simulation/initial_conditions.py b/examples/Basic_Simulation/initial_conditions.py
@@ -1,5 +1,5 @@
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.

diff --git a/examples/Basic_Simulation/output_reader.py b/examples/Basic_Simulation/output_reader.py
@@ -1,5 +1,5 @@
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.

diff --git a/examples/Chambers2013/init_cond.py b/examples/Chambers2013/init_cond.py
@@ -1,3 +1,14 @@
+"""
+ 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. 
+"""
+
 #!/usr/bin/env python3
 import swiftest
 import numpy as np

diff --git a/examples/Chambers2013/scattermovie.py b/examples/Chambers2013/scattermovie.py
@@ -1,3 +1,14 @@
+"""
+ 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. 
+"""
+
 #!/usr/bin/env python3
 import swiftest 
 import numpy as np

diff --git a/examples/Fragmentation/Fragmentation_Movie.py b/examples/Fragmentation/Fragmentation_Movie.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.
@@ -152,20 +152,20 @@ def encounter_combiner(sim):
     ds = xr.combine_nested([data,enc],concat_dim='time').sortby("time").interpolate_na(dim="time")
 
     # Rename the merged Target body so that their data can be combined
-    tname=[n for n in ds['name'].data if "Target" in n]
-    nottname=[n for n in ds['name'].data if "Target" not in n]
+    tname=[n for n in ds['name'].data if names[0] in n]
+    nottname=[n for n in ds['name'].data if names[0] not in n]
     dslist = []
     for n in tname:
         dsnew = ds.sel(name=n)
-        dsnew['name'] = "Target"
+        dsnew['name'] = names[0]
         dslist.append(dsnew)
 
     newds = xr.merge(dslist,compat="no_conflicts") 
     ds = xr.combine_nested([ds.sel(name=nottname),newds],concat_dim="name")
 
     # Interpolate in time to make a smooth, constant time step dataset 
     # Add a bit of padding to the time, otherwise there are some issues with the interpolation in the last few frames.
-    smooth_time = np.linspace(start=tgood.isel(time=0), stop=ds.time[-1], num=int(1.2*num_movie_frames))
+    smooth_time = np.linspace(start=ds.time[0], stop=ds.time[-1], num=int(1.2*num_movie_frames))
     ds = ds.interp(time=smooth_time)
     ds['rotangle'] = xr.zeros_like(ds['rot'])
     ds['rot'] = ds['rot'].fillna(0.0)
@@ -183,7 +183,7 @@ class AnimatedScatter(object):
     """An animated scatter plot using matplotlib.animations.FuncAnimation."""
 
     def __init__(self, sim, animfile, title, style, nskip=1):
-
+        self.sim = sim
         self.ds = encounter_combiner(sim)
         self.npl = len(self.ds['name']) - 1
         self.title = title
@@ -206,8 +206,8 @@ def setup_plot(self):
 
         # Calculate the distance along the y-axis between the colliding bodies at the start of the simulation.
         # This will be used to scale the axis limits on the movie.
-        rhy1 = self.ds['rh'].sel(name="Target",space='y').isel(time=0).values[()]
-        rhy2 = self.ds['rh'].sel(name="Projectile",space='y').isel(time=0).values[()]
+        rhy1 = self.sim.data['rh'].sel(name=names[0],space='y').isel(time=0).values[()]
+        rhy2 = self.sim.data['rh'].sel(name=names[1],space='y').isel(time=0).values[()]
 
         scale_frame =   abs(rhy1) + abs(rhy2)
         if "hitandrun" in style:

diff --git a/examples/Fragmentation/Multibody_Movie.py b/examples/Fragmentation/Multibody_Movie.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.

diff --git a/examples/Fragmentation/swiftest_fragmentation.py b/examples/Fragmentation/swiftest_fragmentation.py
@@ -1,5 +1,5 @@
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.

diff --git a/examples/Swifter_Swiftest/cb.in b/examples/Swifter_Swiftest/cb.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/param.swifter.in b/examples/Swifter_Swiftest/param.swifter.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/param.swiftest.in b/examples/Swifter_Swiftest/param.swiftest.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/pl.swifter.in b/examples/Swifter_Swiftest/pl.swifter.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/pl.swiftest.in b/examples/Swifter_Swiftest/pl.swiftest.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/swifter_start.in b/examples/Swifter_Swiftest/swifter_start.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/swifter_swiftest_comp.py b/examples/Swifter_Swiftest/swifter_swiftest_comp.py
@@ -1,5 +1,5 @@
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.

diff --git a/examples/Swifter_Swiftest/tp.swifter.in b/examples/Swifter_Swiftest/tp.swifter.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/Swifter_Swiftest/tp.swiftest.in b/examples/Swifter_Swiftest/tp.swiftest.in
@@ -1,4 +1,4 @@
-!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! 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.

diff --git a/examples/helio_gr_test/helio_gr_test.py b/examples/helio_gr_test/helio_gr_test.py
@@ -1,5 +1,5 @@
 """
- Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+ 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.

diff --git a/examples/helio_neptune_pluto/param.in b/examples/helio_neptune_pluto/param.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 ! VERSION        Swiftest parameter input from file param.in
 T0               0.0
 TSTOP            100000.0

diff --git a/examples/symba_swifter_comparison/1pl_1pl_collision/param.swiftest.in b/examples/symba_swifter_comparison/1pl_1pl_collision/param.swiftest.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 ! VERSION        Swiftest parameter input
 T0               0.0
 TSTOP            1.0

diff --git a/examples/symba_swifter_comparison/1pl_1pl_collision/pl.swiftest.in b/examples/symba_swifter_comparison/1pl_1pl_collision/pl.swiftest.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 2
 Mercury 6.553709809565314146e-06 0.0014751274547839194341
 1.6306381826061645943e-05

diff --git a/examples/symba_swifter_comparison/1pl_1pl_collision/sun_MsunAUYR.in b/examples/symba_swifter_comparison/1pl_1pl_collision/sun_MsunAUYR.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 Sun
 39.476926408897626
 0.004650467260962157

diff --git a/examples/symba_swifter_comparison/1pl_1pl_collision/tp.swiftest.in b/examples/symba_swifter_comparison/1pl_1pl_collision/tp.swiftest.in
@@ -1 +1,10 @@
+!! 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. 
+
 0
diff --git a/examples/symba_swifter_comparison/1pl_1tp_collision/param.swiftest.in b/examples/symba_swifter_comparison/1pl_1tp_collision/param.swiftest.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 ! VERSION        Swiftest parameter input
 T0               0.0
 TSTOP            1.0

diff --git a/examples/symba_swifter_comparison/1pl_1tp_collision/pl.swiftest.in b/examples/symba_swifter_comparison/1pl_1tp_collision/pl.swiftest.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 1
 Mercury 6.553709809565314146e-06 0.0014751274547839194341
 1.6306381826061645943e-05

diff --git a/examples/symba_swifter_comparison/1pl_1tp_collision/sun_MsunAUYR.in b/examples/symba_swifter_comparison/1pl_1tp_collision/sun_MsunAUYR.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 Sun
 39.476926408897626
 0.004650467260962157

diff --git a/examples/symba_swifter_comparison/1pl_1tp_collision/tp.swiftest.in b/examples/symba_swifter_comparison/1pl_1tp_collision/tp.swiftest.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 1
 Test_Particle
 0.38710350131956905 0.20558985105084426 7.0037441475892

diff --git a/examples/symba_swifter_comparison/8pl/cb.in b/examples/symba_swifter_comparison/8pl/cb.in
@@ -1,3 +1,12 @@
+!! 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. 
+
 Sun
 0.00029591220819207774
 0.004650467260962157