Merge branch 'encounter_storage' into debug

.gitignore

@@ -2,7 +2,6 @@
 *
 # Now, whitelist anything that's a directory
 !*/
-!*/python
 # whitelist only the files that ever need to be tracked
 !*.f90
 !*.sh
@@ -13,72 +12,19 @@
 !paper/paper.md
 !paper/paper.bib
 !README.swifter 
-!*.in
 dump*
-!example/cleanup
-!example/swifter_symba_omp
-!Makefile
-src/*/Makefile
-!Makefile.Defines
-src/*/Makefile.Defines
-!.gitignore
+!**/.gitignore
 !*.py
 !*.ipynb
+!examples/**
 *ipynb_checkpoints
-
-#fxdr library
-!fxdr*/*.c
-!fxdr*/*.F
-!fxdr*/*.3f
-!fxdr*/*.h
-!fxdr*/*.inc
-!fxdr*/cxdrreal64
-!fxdr*/test.orig.xdr
-!fxdr*/test_read_only.xdr
-!fxdr*/configure/
-!fxdr*/README*
-!fxdr*/Makefile.bak
-!fxdr*/Makefile.fxdr
-!fxdr*/Makefile.tmpl
-!fxdr*/Defines.*
-
-#collresolve
-!collresolve/*.c
-!collresolve/*.h
-!collresolve/*.py
-!collresolve/Makefile.am
-!collresolve/configure.ac
-!collresolve/cambioni2019/*.h
-!collresolve/cambioni2019/*.c
-collresolve/config.h
-
-
+**/.DS_Store
 
 #Documentation
 !docs/*
 !docs/*/*
 !docs/*/*/*
 !README_figs/*
 
-python/swiftest/tests/convert_code_type/swift2swifter/pl.swift2swifter.in
-
-python/swiftest/tests/convert_code_type/swift2swifter/tp.swift2swifter.in
-
-python/swiftest/tests/convert_code_type/swift2swiftest/cb.swift2swiftest.in
-
-python/swiftest/tests/convert_code_type/swift2swiftest/pl.swift2swiftest.in
-
-python/swiftest/tests/convert_code_type/swift2swiftest/tp.swift2swiftest.in
-
-python/swiftest/tests/convert_code_type/swifter2swiftest/cb.swifter2swiftest.in
-
-python/swiftest/tests/convert_code_type/cb.swifter2swiftest.in
-
-python/swiftest/tests/convert_code_type/swifter2swiftest/pl.swifter2swiftest.in
-
-python/swiftest/tests/convert_code_type/swifter2swiftest/tp.swifter2swiftest.in
-
-!python/swiftest/requirements.txt
-
 bin/
 build/*

examples/.gitignore

@@ -1,4 +1,6 @@
-*/param.*
-*/simdata/*
-*/*/simdata/*
-
+*
+!.gitignore
+!Basic_Simulation/*
+!Fragmentation/*
+!helio_gr_test/*
+!whm_gr_test/*

examples/Basic_Simulation/.gitignore

@@ -0,0 +1,6 @@
+*
+!.gitignore
+!initial_conditions.py
+!output_reader.py
+!run_from_file.py
+!read_old_run.py

examples/Fragmentation/.gitignore

@@ -0,0 +1,3 @@
+*
+!.gitignore
+!Fragmentation_Movie.py

examples/Fragmentation/Fragmentation_Movie.py

@@ -40,8 +40,8 @@
 movie_titles = dict(zip(available_movie_styles, movie_title_list))
 
 # These initial conditions were generated by trial and error
-pos_vectors = {"disruption_headon"         : [np.array([1.0, -1.807993e-05, 0.0]),
-                                              np.array([1.0,  1.807993e-05 ,0.0])],
+pos_vectors = {"disruption_headon"         : [np.array([1.0, -2.807993e-05, 0.0]),
+                                              np.array([1.0,  2.807993e-05 ,0.0])],
                "supercatastrophic_off_axis": [np.array([1.0, -4.2e-05,      0.0]),
                                               np.array([1.0,  4.2e-05,      0.0])],
                "hitandrun"                 : [np.array([1.0, -2.0e-05,      0.0]),
@@ -84,7 +84,9 @@ class AnimatedScatter(object):
     """An animated scatter plot using matplotlib.animations.FuncAnimation."""
 
     def __init__(self, sim, animfile, title, nskip=1):
-        nframes = int(sim.data['time'].size)
+        tgood = sim.enc.where(sim.enc['Gmass'] > 9e-8).time
+        self.ds = sim.enc.sel(time=tgood)
+        nframes = int(self.ds['time'].size)
         self.sim = sim
         self.title = title
         self.body_color_list = {'Initial conditions': 'xkcd:windows blue',
@@ -106,13 +108,14 @@ def setup_plot(self):
         fig = plt.figure(figsize=figsize, dpi=300)
         plt.tight_layout(pad=0)
 
-
         # 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.
-        scale_frame =   abs(sim.data['xhy'].isel(time=0, name=1).values) \
-                      + abs( sim.data['xhy'].isel(time=0, name=2).values)
+        rhy1 = self.ds['rh'].sel(name="Body1",space='y').isel(time=0).values[()]
+        rhy2 = self.ds['rh'].sel(name="Body2",space='y').isel(time=0).values[()]
+
+        scale_frame =   abs(rhy1) + abs(rhy2)
         ax = plt.Axes(fig, [0.1, 0.1, 0.8, 0.8])
-        self.ax_pt_size = figsize[0] * 0.8 *  72 / scale_frame
+        self.ax_pt_size = figsize[0] * 0.8 *  72 / (2 * scale_frame)
         ax.set_xlim(-scale_frame, scale_frame)
         ax.set_ylim(-scale_frame, scale_frame)
         ax.set_xticks([])
@@ -131,19 +134,20 @@ def center(Gmass, x, y):
             x = x[~np.isnan(x)]
             y = y[~np.isnan(y)]
             Gmass = Gmass[~np.isnan(Gmass)]
+            x = x[Gmass]
             x_com = np.sum(Gmass * x) / np.sum(Gmass)
-            y_com = np.sum(Gmass * y) / np.sum(Gmass)
+            y_com = #np.sum(Gmass * y) / np.sum(Gmass)
             return x_com, y_com
 
         Gmass, rh, point_rad = next(self.data_stream(frame))
-        x_com, y_com = center(Gmass, rh[:,1], rh[:,2])
-        self.scatter_artist.set_offsets(np.c_[x - x_com, y - y_com])
-        self.scatter_artist.set_sizes(point_rad)
+        #x_com, y_com = center(Gmass, rh[:,0], rh[:,1])
+        self.scatter_artist.set_offsets(np.c_[rh[:,0] - x_com, rh[:,1] - y_com])
+        self.scatter_artist.set_sizes(point_rad**2)
         return self.scatter_artist,
 
     def data_stream(self, frame=0):
         while True:
-            ds = self.sim.data.isel(time=frame)
+            ds = self.ds.isel(time=frame)
             ds = ds.where(ds['name'] != "Sun", drop=True)
             radius = ds['radius'].values
             Gmass = ds['Gmass'].values
@@ -153,47 +157,30 @@ def data_stream(self, frame=0):
 
 if __name__ == "__main__":
 
-   print("Select a fragmentation movie to generate.")
-   print("1. Head-on disruption")
-   print("2. Off-axis supercatastrophic")
-   print("3. Hit and run")
-   print("4. All of the above")
-   user_selection = int(input("? "))
-
-   if user_selection > 0 and user_selection < 4:
-      movie_styles = [available_movie_styles[user_selection-1]]
-   else:
-      print("Generating all movie styles")
-      movie_styles = available_movie_styles.copy()
-
-   for style in movie_styles:
-       bin_file = Path(style) / "bin.nc"
-       if bin_file.exists():
-           user_selection = input(f"An older simulation of {movie_titles[style]} exists. Do you want to re-run it? [y/N] ")
-           if user_selection == "":
-               run_new = False
-           else:
-               try:
-                   run_new = swiftest.io.str2bool(user_selection)
-               except:
-                   run_new = False
-       else:
-           run_new = True
-
-       movie_filename = f"{style}.mp4"
-
-       # Pull in the Swiftest output data from the parameter file and store it as a Xarray dataset.
-       if run_new:
-           sim = swiftest.Simulation(simdir=style, rotation=True, init_cond_format = "XV", compute_conservation_values=True)
-           sim.add_solar_system_body("Sun")
-           sim.add_body(Gmass=body_Gmass[style], radius=body_radius[style], rh=pos_vectors[style], vh=vel_vectors[style]) #, rot=rot_vectors[style])
-
-           # Set fragmentation parameters
-           minimum_fragment_gmass = 0.2 * body_Gmass[style][1] # Make the minimum fragment mass a fraction of the smallest body
-           gmtiny = 0.99 * body_Gmass[style][1] # Make GMTINY just smaller than the smallest original body. This will prevent runaway collisional cascades
-           sim.set_parameter(fragmentation = True, gmtiny=gmtiny, minimum_fragment_gmass=minimum_fragment_gmass, verbose=False)
-           sim.run(dt=2e-5, tstop=2.e-5)
-       else:
-           sim = swiftest.Simulation(param_file=param_file, read_old_output_file=True)
-
-       anim = AnimatedScatter(sim,movie_filename,movie_titles[style],nskip=10)
+    print("Select a fragmentation movie to generate.")
+    print("1. Head-on disruption")
+    print("2. Off-axis supercatastrophic")
+    print("3. Hit and run")
+    print("4. All of the above")
+    user_selection = int(input("? "))
+
+    if user_selection > 0 and user_selection < 4:
+       movie_styles = [available_movie_styles[user_selection-1]]
+    else:
+       print("Generating all movie styles")
+       movie_styles = available_movie_styles.copy()
+
+    for style in movie_styles:
+        movie_filename = f"{style}.mp4"
+        # Pull in the Swiftest output data from the parameter file and store it as a Xarray dataset.
+        sim = swiftest.Simulation(simdir=style, rotation=True, init_cond_format = "XV", compute_conservation_values=True)
+        sim.add_solar_system_body("Sun")
+        sim.add_body(Gmass=body_Gmass[style], radius=body_radius[style], rh=pos_vectors[style], vh=vel_vectors[style]) #, rot=rot_vectors[style])
+        #
+        # Set fragmentation parameters
+        minimum_fragment_gmass = 0.2 * body_Gmass[style][1] # Make the minimum fragment mass a fraction of the smallest body
+        gmtiny = 0.99 * body_Gmass[style][1] # Make GMTINY just smaller than the smallest original body. This will prevent runaway collisional cascades
+        sim.set_parameter(fragmentation=True, fragmentation_save="TRAJECTORY", gmtiny=gmtiny, minimum_fragment_gmass=minimum_fragment_gmass, verbose=False)
+        sim.run(dt=1e-4, tstop=2.0e-3, istep_out=1, dump_cadence=0)
+
+        anim = AnimatedScatter(sim,movie_filename,movie_titles[style],nskip=1)

examples/helio_gr_test/.gitignore

@@ -0,0 +1,3 @@
+*
+!.gitignore
+!helio_gr_test.py

examples/whm_gr_test/.gitignore

@@ -0,0 +1,3 @@
+*
+!.gitignore
+!whm_gr_test.py