Fixed more bugs in encounter data processing

examples/.gitignore

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

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, -2.807993e-05, 0.0]),
-                                              np.array([1.0,  2.807993e-05 ,0.0])],
+pos_vectors = {"disruption_headon"         : [np.array([1.0, -5.0e-05, 0.0]),
+                                              np.array([1.0,  5.0e-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]),
@@ -185,6 +185,6 @@ def data_stream(self, frame=0):
         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)
+        sim.run(dt=1e-4, tstop=4.0e-3, istep_out=1, dump_cadence=0)
 
         anim = AnimatedScatter(sim,movie_filename,movie_titles[style],style,nskip=1)

python/swiftest/swiftest/simulation_class.py

@@ -17,6 +17,7 @@
 from swiftest import __file__ as _pyfile
 import json
 import os
+from glob import glob
 from pathlib import Path
 import datetime
 import xarray as xr
@@ -2667,23 +2668,23 @@ def convert(self, param_file, newcodename="Swiftest", plname="pl.swiftest.in", t
 
         Parameters
         ----------
-           param_file : string
-                File name of the input parameter file
-            newcodename : string
-                Name of the desired format (Swift/Swifter/Swiftest)
-            plname : string
-                File name of the massive body input file
-            tpname : string
-                File name of the test particle input file
-            cbname : string
-                File name of the central body input file
-            conversion_questions : dictronary
-                Dictionary of additional parameters required to convert between formats
+        param_file : string
+        File name of the input parameter file
+        newcodename : string
+        Name of the desired format (Swift/Swifter/Swiftest)
+        plname : string
+        File name of the massive body input file
+        tpname : string
+        File name of the test particle input file
+        cbname : string
+        File name of the central body input file
+        conversion_questions : dictronary
+        Dictionary of additional parameters required to convert between formats
 
         Returns
         -------
-            oldparam : xarray dataset
-                The old parameter configuration.
+        oldparam : xarray dataset
+        The old parameter configuration.
         """
         oldparam = self.param
         if self.codename == newcodename:
@@ -2720,12 +2721,12 @@ def read_output_file(self,read_init_cond : bool = True):
 
         Parameters
         ----------
-            read_init_cond : bool
-                Read in an initial conditions file along with the output file. Default is True
+        read_init_cond : bool
+        Read in an initial conditions file along with the output file. Default is True
 
         Returns
         -------
-            self.data : xarray dataset
+        self.data : xarray dataset
         """
 
         # Make a temporary copy of the parameter dictionary so we can supply the absolute path of the binary file
@@ -2765,7 +2766,8 @@ def read_output_file(self,read_init_cond : bool = True):
     def read_encounter(self):
         if self.verbose:
             print("Reading encounter history file as .enc")
-        enc_files = self.simdir.glob("**/encounter_*.nc")
+        enc_files = glob(f"{self.simdir}{os.path.sep}encounter_*.nc")
+        enc_files.sort()
 
         # This is needed in order to pass the param argument down to the io.process_netcdf_input function
         def _preprocess(ds, param):
@@ -2774,6 +2776,9 @@ def _preprocess(ds, param):
 
         self.enc = xr.open_mfdataset(enc_files,parallel=True,combine="nested",concat_dim="time",join="left",preprocess=partial_func,mask_and_scale=True)
         self.enc = io.process_netcdf_input(self.enc, self.param)
+        # Remove any overlapping time values
+        tgood,tid = np.unique(self.enc.time,return_index=True)
+        self.enc = self.enc.isel(time=tid)
 
         return