Lots of refactoring. Changed bin.nc to data.nc. Changed .ic to .init_…

…cond. Changed the way encounter and collisions are read in (always read the files in if they exist)

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
 ------

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/simulation_class.py

@@ -141,8 +141,7 @@ def __init__(self,read_param: bool = False, read_old_output: bool = False, simdi
             Parameter input file equivalent: `OUT_TYPE`
         output_file_name : str or path-like, optional
             Name of output file to generate. If not supplied, then one of the default file names are used, depending on
-            the value passed to `output_file_type`. If one of the NetCDF types are used, the default is "bin.nc".
-            Otherwise, the default is "bin.dat".
+            the value passed to `output_file_type`. The default is "data.nc".
             Parameter input file equivalent: `BIN_OUT`
         output_format : {"XV","XVEL"}, default "XVEL"
             Specifies the format for the data saved to the output file. If "XV" then cartesian position and velocity
@@ -312,7 +311,7 @@ def __init__(self,read_param: bool = False, read_old_output: bool = False, simdi
 
         self.param = {}
         self.data = xr.Dataset()
-        self.ic = xr.Dataset()
+        self.init_cond = xr.Dataset()
         self.encounters = xr.Dataset()
         self.collisions = xr.Dataset()
 
@@ -1508,7 +1507,7 @@ def set_output_files(self,
             * Swift: Only "REAL4" supported.
         output_file_name : str or path-like, optional
             Name of output file to generate. If not supplied, then one of the default file names are used, depending on
-            the value passed to `output_file_type`. If one of the NetCDF types are used, the default is "bin.nc".
+            the value passed to `output_file_type`. If one of the NetCDF types are used, the default is "data.nc".
             Otherwise, the default is "bin.dat".
         output_format : {"XV","XVEL"}, optional
             Specifies the format for the data saved to the output file. If "XV" then cartesian position and velocity
@@ -1568,7 +1567,7 @@ def set_output_files(self,
         self.param['OUT_TYPE'] = output_file_type
         if output_file_name is None:
             if output_file_type in ["NETCDF_DOUBLE", "NETCDF_FLOAT"]:
-                self.param['BIN_OUT'] = "bin.nc"
+                self.param['BIN_OUT'] = "data.nc"
             else:
                 self.param['BIN_OUT'] = "bin.dat"
         else:
@@ -2157,7 +2156,7 @@ def add_solar_system_body(self,
         if dsnew['npl'] > 0 or dsnew['ntp'] > 0:
            self.save(verbose=False)
 
-        self.ic = self.data.copy(deep=True)
+        self.init_cond = self.data.copy(deep=True)
 
         return
 
@@ -2456,7 +2455,7 @@ def input_to_array_3d(val,n=None):
 
         dsnew = self._combine_and_fix_dsnew(dsnew)
         self.save(verbose=False)
-        self.ic = self.data.copy(deep=True)
+        self.init_cond = self.data.copy(deep=True)
 
         return
 
@@ -2563,7 +2562,7 @@ def read_param(self,
                        param_tmp = self.param.copy()
                        param_tmp['BIN_OUT'] = init_cond_file
                        self.data = io.swiftest2xr(param_tmp, verbose=self.verbose)
-                       self.ic = self.data.copy(deep=True)
+                       self.init_cond = self.data.copy(deep=True)
                    else:
                        warnings.warn(f"Initial conditions file file {init_cond_file} not found.", stacklevel=2)
                 else:
@@ -2706,29 +2705,22 @@ def read_output_file(self,read_init_cond : bool = True):
         # This is done to handle cases where the method is called from a different working directory than the simulation
         # results
 
-        if "ENCOUNTER_SAVE" in self.param:
-            read_encounters = self.param["ENCOUNTER_SAVE"] != "NONE"
-        else:
-            read_encounters = False
-
         param_tmp = self.param.copy()
         param_tmp['BIN_OUT'] = os.path.join(self.simdir, self.param['BIN_OUT'])
         if self.codename == "Swiftest":
             self.data = io.swiftest2xr(param_tmp, verbose=self.verbose)
             if self.verbose: print('Swiftest simulation data stored as xarray DataSet .data')
             if read_init_cond:
                 if self.verbose:
-                    print("Reading initial conditions file as .ic")
+                    print("Reading initial conditions file as .init_cond")
                 if "NETCDF" in self.param['IN_TYPE']:
                     param_tmp['BIN_OUT'] = self.simdir / self.param['NC_IN']
-
-                    self.ic = io.swiftest2xr(param_tmp, verbose=self.verbose)
+                    self.init_cond = io.swiftest2xr(param_tmp, verbose=False)
                 else:
-                    self.ic = self.data.isel(time=0)
-            if read_encounters:
-                self.read_encounters()
-            if read_collisions:
-                self.read_collisions()
+                    self.init_cond = self.data.isel(time=0)
+
+            self.read_encounters()
+            self.read_collisions()
 
         elif self.codename == "Swifter":
             self.data = io.swifter2xr(param_tmp, verbose=self.verbose)
@@ -2740,9 +2732,13 @@ def read_output_file(self,read_init_cond : bool = True):
         return
 
     def read_encounters(self):
+        enc_files = glob(f"{self.simdir}{os.path.sep}encounter_*.nc")
+        if len(enc_files) == 0:
+            return
+
         if self.verbose:
             print("Reading encounter history file as .encounters")
-        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
@@ -2760,10 +2756,13 @@ def _preprocess(ds, param):
 
 
     def read_collisions(self):
-        if self.verbose:
-                print("Reading collision history file as .collisions")
         col_files = glob(f"{self.simdir}{os.path.sep}collision_*.nc")
+        if len(col_files) == 0:
+            return
+
         col_files.sort()
+        if self.verbose:
+                print("Reading collision history file as .collisions")
 
         # This is needed in order to pass the param argument down to the io.process_netcdf_input function
         def _preprocess(ds, param):

src/modules/swiftest_globals.f90

@@ -122,7 +122,7 @@ module swiftest_globals
    character(*), parameter :: PL_INFILE        = 'pl.in'
    character(*), parameter :: TP_INFILE        = 'tp.in'
    character(*), parameter :: NC_INFILE        = 'in.nc'
-   character(*), parameter :: BIN_OUTFILE      = 'bin.nc'
+   character(*), parameter :: BIN_OUTFILE      = 'data.nc'
    integer(I4B), parameter :: BINUNIT          = 20 !! File unit number for the binary output file
    integer(I4B), parameter :: PARTICLEUNIT     = 44 !! File unit number for the binary particle info output file
    integer(I4B), parameter :: LUN              = 42 !! File unit number for files that are opened and closed within a single subroutine call, and therefore should not collide