Merge branch 'encounter_storage' into debug

examples/Basic_Simulation/initial_conditions.py

@@ -20,7 +20,7 @@
 
 Output
 ------
-bin.nc         : A NetCDF file containing the simulation 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.

examples/Basic_Simulation/output_reader.py

@@ -15,7 +15,7 @@
 
 Input
 ------
-bin.nc     : A NetCDF file containing the simulation output.
+data.nc     : A NetCDF file containing the simulation output.
 
 Output
 ------
@@ -28,7 +28,7 @@
 import matplotlib.pyplot as plt
 
 # Read in the simulation output and store it as an Xarray dataset.
-sim = swiftest.Simulation(read_old_output_file=True)
+sim = swiftest.Simulation(read_old_output=True)
 
 # Plot of the data and save the output plot.
 colors = ['white' if x == 'Massive Body' else 'black' for x in sim.data['particle_type']]

examples/Fragmentation/Fragmentation_Movie.py

@@ -90,7 +90,7 @@ def encounter_combiner(sim):
     # Only keep a minimal subset of necessary data from the simulation and encounter datasets
     keep_vars = ['rh','Gmass','radius']
     data = sim.data[keep_vars]
-    enc = sim.enc[keep_vars].load()
+    enc = sim.encounters[keep_vars].load()
 
     # Remove any encounter data at the same time steps that appear in the data to prevent duplicates
     t_not_duplicate = ~enc['time'].isin(data['time'])
@@ -148,7 +148,7 @@ def setup_plot(self):
         ax.set_title(self.title)
         fig.add_axes(ax)
 
-        self.scatter_artist = ax.scatter([], [], animated=True)
+        self.scatter_artist = ax.scatter([], [], animated=True, c='k', edgecolors='face')
         return fig, ax
 
     def update_plot(self, frame):
@@ -174,7 +174,7 @@ def data_stream(self, frame=0):
             radius = ds['radius'].values
             Gmass = ds['Gmass'].values
             rh = ds['rh'].values
-            point_rad = 2 * radius * self.ax_pt_size
+            point_rad = radius * self.ax_pt_size
             yield Gmass, rh, point_rad
 
 if __name__ == "__main__":
@@ -202,8 +202,8 @@ def data_stream(self, frame=0):
         # 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=1.0e-3, istep_out=1, dump_cadence=0)
+        sim.set_parameter(fragmentation=True, encounter_save="trajectory", gmtiny=gmtiny, minimum_fragment_gmass=minimum_fragment_gmass, verbose=False)
+        sim.run(dt=1e-4, tstop=1.0e-3, istep_out=1, dump_cadence=1)
 
         print("Generating animation")
         anim = AnimatedScatter(sim,movie_filename,movie_titles[style],style,nskip=1)

examples/Fragmentation/swiftest_fragmentation.py

@@ -21,7 +21,7 @@
 
 Output
 ------
-disruption/bin.nc         : A NetCDF file containing the simulation output.
+disruption/data.nc         : A NetCDF file containing the simulation output.
 disruption/dump_bin1.nc   : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 disruption/dump_bin2.nc   : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 disruption/dump_param1.in : An ASCII file containing the necessary parameters to restart a simulation.
@@ -30,7 +30,7 @@
 disruption/init_cond.nc   : A NetCDF file containing the initial conditions for the simulation.
 disruption/param.in       : An ASCII file containing the parameters for the simulation.
 disruption/swiftest.log   : An ASCII file containing the information on the status of the simulation as it runs.
-hitandrun/bin.nc          : A NetCDF file containing the simulation output.
+hitandrun/data.nc          : A NetCDF file containing the simulation output.
 hitandrun/dump_bin1.nc    : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 hitandrun/dump_bin2.nc    : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 hitandrun/dump_param1.in  : An ASCII file containing the necessary parameters to restart a simulation.
@@ -39,7 +39,7 @@
 hitandrun/init_cond.nc    : A NetCDF file containing the initial conditions for the simulation.
 hitandrun/param.in        : An ASCII file containing the parameters for the simulation.
 hitandrun/swiftest.log    : An ASCII file containing the information on the status of the simulation as it runs.
-supercat/bin.nc           : A NetCDF file containing the simulation output.
+supercat/data.nc           : A NetCDF file containing the simulation output.
 supercat/dump_bin1.nc     : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 supercat/dump_bin2.nc     : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 supercat/dump_param1.in   : An ASCII file containing the necessary parameters to restart a simulation.

examples/helio_gr_test/helio_gr_test.py

@@ -24,15 +24,15 @@
 helio_gr_mercury_precession.png : Portable Network Graphic file depicting the precession of Mercury's perihelion over time
                                   with data sourced from the JPL Horizons database, Swiftest run with general relativity, 
                                   and Swiftest run without general relativity.
-gr/bin.nc                       : A NetCDF file containing the simulation output.
+gr/data.nc                       : A NetCDF file containing the simulation output.
 gr/dump_bin1.nc                 : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 gr/dump_bin2.nc                 : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 gr/dump_param1.in               : An ASCII file containing the necessary parameters to restart a simulation.
 gr/dump_param2.in               : An ASCII file containing the necessary parameters to restart a simulation.
 gr/init_cond.nc                 : A NetCDF file containing the initial conditions for the simulation.
 gr/param.in                     : An ASCII file containing the parameters for the simulation.
 gr/swiftest.log                 : An ASCII file containing the information on the status of the simulation as it runs.
-nogr/bin.nc                     : A NetCDF file containing the simulation output.
+nogr/data.nc                     : A NetCDF file containing the simulation output.
 nogr/dump_bin1.nc               : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 nogr/dump_bin2.nc               : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 nogr/dump_param1.in             : An ASCII file containing the necessary parameters to restart a simulation.

examples/whm_gr_test/whm_gr_test.py

@@ -24,15 +24,15 @@
 whm_gr_mercury_precession.png : Portable Network Graphic file depicting the precession of Mercury's perihelion over time
                                 with data sourced from the JPL Horizons database, Swiftest run with general relativity, 
                                 and Swiftest run without general relativity.
-gr/bin.nc                     : A NetCDF file containing the simulation output.
+gr/data.nc                     : A NetCDF file containing the simulation output.
 gr/dump_bin1.nc               : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 gr/dump_bin2.nc               : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 gr/dump_param1.in             : An ASCII file containing the necessary parameters to restart a simulation.
 gr/dump_param2.in             : An ASCII file containing the necessary parameters to restart a simulation.
 gr/init_cond.nc               : A NetCDF file containing the initial conditions for the simulation.
 gr/param.in                   : An ASCII file containing the parameters for the simulation.
 gr/swiftest.log               : An ASCII file containing the information on the status of the simulation as it runs.
-nogr/bin.nc                   : A NetCDF file containing the simulation output.
+nogr/data.nc                   : A NetCDF file containing the simulation output.
 nogr/dump_bin1.nc             : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 nogr/dump_bin2.nc             : A NetCDF file containing the necessary inputs to restart a simulation from t!=0.
 nogr/dump_param1.in           : An ASCII file containing the necessary parameters to restart a simulation.

python/swiftest/swiftest/io.py

@@ -32,8 +32,7 @@
                   "ENCOUNTER_CHECK",
                   "TSTART",
                   "DUMP_CADENCE",
-                  "ENCOUNTER_SAVE",
-                  "FRAGMENTATION_SAVE")
+                  "ENCOUNTER_SAVE")
 
 
 
@@ -55,16 +54,16 @@
 float_param = ["T0", "TSTART", "TSTOP", "DT", "CHK_RMIN", "CHK_RMAX", "CHK_EJECT", "CHK_QMIN", "DU2M", "MU2KG",
                "TU2S", "MIN_GMFRAG", "GMTINY"]
 
-upper_str_param = ["OUT_TYPE","OUT_FORM","OUT_STAT","IN_TYPE","IN_FORM","ENCOUNTER_SAVE","FRAGMENTATION_SAVE", "CHK_QMIN_COORD"]
+upper_str_param = ["OUT_TYPE","OUT_FORM","OUT_STAT","IN_TYPE","IN_FORM","ENCOUNTER_SAVE", "CHK_QMIN_COORD"]
 lower_str_param = ["NC_IN", "PL_IN", "TP_IN", "CB_IN", "CHK_QMIN_RANGE"]
 
 param_keys = ['! VERSION'] + int_param + float_param + upper_str_param + lower_str_param+ bool_param
 
 # This defines Xarray Dataset variables that are strings, which must be processed due to quirks in how NetCDF-Fortran
 # handles strings differently than Python's Xarray.
-string_varnames = ["name", "particle_type", "status", "origin_type"]
+string_varnames = ["name", "particle_type", "status", "origin_type", "stage", "regime"]
 char_varnames = ["space"]
-int_varnames = ["id", "ntp", "npl", "nplm", "discard_body_id", "collision_id"]
+int_varnames = ["id", "ntp", "npl", "nplm", "discard_body_id", "collision_id", "loopnum"]
 
 def bool2yesno(boolval):
     """
@@ -816,18 +815,19 @@ def process_netcdf_input(ds, param):
     -------
     ds : xarray dataset
     """
-
-    ds = ds.where(~np.isnan(ds.id) ,drop=True)
+    #
+    #ds = ds.where(ds.id >=0,drop=True)
     if param['OUT_TYPE'] == "NETCDF_DOUBLE":
         ds = fix_types(ds,ftype=np.float64)
     elif param['OUT_TYPE'] == "NETCDF_FLOAT":
         ds = fix_types(ds,ftype=np.float32)
 
-    # Check if the name variable contains unique values. If so, make name the dimension instead of id
-    if "id" in ds.dims:
-        if len(np.unique(ds['name'])) == len(ds['name']):
-            ds = ds.swap_dims({"id" : "name"})
-            ds = ds.reset_coords("id")
+    # # Check if the name variable contains unique values. If so, make name the dimension instead of id
+    # if "id" in ds.dims:
+    #     if len(np.unique(ds['name'])) == len(ds['name']):
+    #         ds = ds.swap_dims({"id" : "name"})
+    #         if "id" in ds:
+    #             ds = ds.reset_coords("id")
 
     return ds
 
@@ -900,15 +900,14 @@ def string_converter(da):
     -------
     da : xarray dataset with the strings cleaned up
     """
-    if da.dtype == np.dtype(object):
-        da = da.astype('<U32')
-        da = xstrip_str(da)
-    elif type(da.values[0]) != np.str_:
-        da = xstrip_nonstr(da)
+
+    da = da.astype('<U32')
+    da = xstrip_str(da)
+
     return da
 
 def char_converter(da):
-    """
+    """`
     Converts a string to a unicode string
 
     Parameters
@@ -1126,9 +1125,6 @@ def swiftest_xr2infile(ds, param, in_type="NETCDF_DOUBLE", infile_name=None,fram
     param_tmp['OUT_FORM'] = param['IN_FORM']
     frame = select_active_from_frame(ds, param_tmp, framenum)
 
-    if "name" in frame.dims:
-        frame = frame.swap_dims({"name" : "id"})
-        frame = frame.reset_coords("name")
 
     if in_type == "NETCDF_DOUBLE" or in_type == "NETCDF_FLOAT":
         # Convert strings back to byte form and save the NetCDF file
@@ -1145,8 +1141,8 @@ def swiftest_xr2infile(ds, param, in_type="NETCDF_DOUBLE", infile_name=None,fram
         return frame
 
     # All other file types need seperate files for each of the inputs
-    cb = frame.where(frame.id == 0, drop=True)
-    pl = frame.where(frame.id > 0, drop=True)
+    cb = frame.isel(name=0)
+    pl = frame.where(name != cb.name)
     pl = pl.where(np.invert(np.isnan(pl['Gmass'])), drop=True).drop_vars(['j2rp2', 'j2rp2'],errors="ignore")
     tp = frame.where(np.isnan(frame['Gmass']), drop=True).drop_vars(['Gmass', 'radius', 'j2rp2', 'j4rp4'],errors="ignore")