Now index by "name" instead of "id" on the Fortran side

examples/Fragmentation/Fragmentation_Movie.py

@@ -202,7 +202,7 @@ 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, collision_save="TRAJECTORY", gmtiny=gmtiny, minimum_fragment_gmass=minimum_fragment_gmass, verbose=False)
+        sim.set_parameter(fragmentation=True, collision_save="TRAJECTORY", 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")

python/swiftest/swiftest/io.py

@@ -817,18 +817,18 @@ def process_netcdf_input(ds, param):
     ds : xarray dataset
     """
     #
-    ds = ds.where(ds.id >=0,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"})
-            if "id" in ds:
-                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
 
@@ -1127,9 +1127,6 @@ 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
@@ -1146,8 +1143,8 @@ 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")
 

python/swiftest/swiftest/simulation_class.py

@@ -2790,11 +2790,6 @@ def _preprocess(ds, param):
         tgood,tid = np.unique(self.encounters.time,return_index=True)
         self.encounters = self.encounters.isel(time=tid)
 
-        # Reduce the dimensionality of variables that got expanded in the combine process
-        self.encounters['loopnum'] = self.encounters['loopnum'].max(dim="name")
-        self.encounters['id'] = self.encounters['id'].max(dim="time")
-        self.encounters['particle_type'] = self.encounters['particle_type'].max(dim="time")
-
         return
 
 
@@ -2809,14 +2804,9 @@ def _preprocess(ds, param):
             return io.process_netcdf_input(ds,param)
         partial_func = partial(_preprocess, param=self.param)
 
-        self.collisions = xr.open_mfdataset(col_files,parallel=True,combine="nested",concat_dim="collision",join="left",preprocess=partial_func,mask_and_scale=True)
+        self.collisions = xr.open_mfdataset(col_files,parallel=True, coords=["collision"], join="inner", preprocess=partial_func,mask_and_scale=True)
         self.collisions = io.process_netcdf_input(self.collisions, self.param)
 
-        # # Reduce the dimensionality of variables that got expanded in the combine process
-        # self.encounters['loopnum'] = self.encounters['loopnum'].max(dim="name")
-        # self.encounters['id'] = self.encounters['id'].max(dim="time")
-        # self.encounters['particle_type'] = self.encounters['particle_type'].max(dim="time")
-
         return
 
 

src/encounter/encounter_io.f90

@@ -29,7 +29,7 @@ module subroutine encounter_io_dump_collision(self, param)
             nc%file_number = nc%file_number + 1 
             call self%make_index_map()
             nc%event_dimsize = self%nt
-            nc%id_dimsize = self%nid
+            nc%name_dimsize = self%nid
 
             write(nc%file_name, '("collision_",I0.6,".nc")') nc%file_number
             call nc%initialize(param)
@@ -73,7 +73,7 @@ module subroutine encounter_io_dump_encounter(self, param)
             nc%file_number = nc%file_number + 1 
             call self%make_index_map()
             nc%time_dimsize = self%nt
-            nc%id_dimsize = self%nid
+            nc%name_dimsize = self%nid
             write(nc%file_name, '("encounter_",I0.6,".nc")') nc%file_number
             call nc%initialize(param)
 
@@ -138,28 +138,28 @@ module subroutine encounter_io_initialize(self, param)
 
          ! Dimensions
          call check( nf90_def_dim(nc%id, nc%time_dimname, nc%time_dimsize, nc%time_dimid), "encounter_io_initialize nf90_def_dim time_dimid" ) ! Simulation time dimension
-         call check( nf90_def_dim(nc%id, nc%space_dimname, NDIM , nc%space_dimid), "encounter_io_initialize nf90_def_dim space_dimid" )           ! 3D space dimension
-         call check( nf90_def_dim(nc%id, nc%id_dimname, nc%id_dimsize, nc%id_dimid), "encounter_io_initialize nf90_def_dim id_dimid" )       ! dimension to store particle id numbers
+         call check( nf90_def_dim(nc%id, nc%space_dimname, NDIM, nc%space_dimid), "encounter_io_initialize nf90_def_dim space_dimid" )           ! 3D space dimension
+         call check( nf90_def_dim(nc%id, nc%name_dimname, nc%name_dimsize, nc%name_dimid), "encounter_io_initialize nf90_def_dim name_dimid" )       ! dimension to store particle id numbers
          call check( nf90_def_dim(nc%id, nc%str_dimname, NAMELEN, nc%str_dimid), "encounter_io_initialize nf90_def_dim str_dimid"  )          ! Dimension for string variables (aka character arrays)
 
          ! Dimension coordinates
          call check( nf90_def_var(nc%id, nc%time_dimname, nc%out_type, nc%time_dimid, nc%time_varid), "encounter_io_initialize nf90_def_var time_varid"  )
          call check( nf90_def_var(nc%id, nc%space_dimname, NF90_CHAR, nc%space_dimid, nc%space_varid), "encounter_io_initialize nf90_def_var space_varid"  )
-         call check( nf90_def_var(nc%id, nc%id_dimname, NF90_INT, nc%id_dimid, nc%id_varid), "encounter_io_initialize nf90_def_var id_varid"  )
+         call check( nf90_def_var(nc%id, nc%name_dimname, NF90_CHAR, [nc%str_dimid, nc%name_dimid], nc%name_varid), "encounter_io_initialize nf90_def_var id_varid"  )
 
          ! Variables
-         call check( nf90_def_var(nc%id, nc%name_varname, NF90_CHAR, [nc%str_dimid, nc%id_dimid], nc%name_varid), "encounter_io_initialize nf90_def_var name_varid"  )
-         call check( nf90_def_var(nc%id, nc%ptype_varname, NF90_CHAR, [nc%str_dimid, nc%id_dimid], nc%ptype_varid), "encounter_io_initialize nf90_def_var ptype_varid"  )
-         call check( nf90_def_var(nc%id, nc%rh_varname,  nc%out_type, [nc%space_dimid, nc%id_dimid, nc%time_dimid], nc%rh_varid), "encounter_io_initialize nf90_def_var rh_varid"  )
-         call check( nf90_def_var(nc%id, nc%vh_varname,  nc%out_type, [nc%space_dimid, nc%id_dimid, nc%time_dimid], nc%vh_varid), "encounter_io_initialize nf90_def_var vh_varid"  )
-         call check( nf90_def_var(nc%id, nc%Gmass_varname, nc%out_type, [nc%id_dimid, nc%time_dimid], nc%Gmass_varid), "encounter_io_initialize nf90_def_var Gmass_varid"  )
+         call check( nf90_def_var(nc%id, nc%id_varname, NF90_INT, nc%name_dimid, nc%id_varid), "encounter_io_initialize nf90_def_var id_varid"  )
+         call check( nf90_def_var(nc%id, nc%ptype_varname, NF90_CHAR, [nc%str_dimid, nc%name_dimid], nc%ptype_varid), "encounter_io_initialize nf90_def_var ptype_varid"  )
+         call check( nf90_def_var(nc%id, nc%rh_varname,  nc%out_type, [nc%space_dimid, nc%name_dimid, nc%time_dimid], nc%rh_varid), "encounter_io_initialize nf90_def_var rh_varid"  )
+         call check( nf90_def_var(nc%id, nc%vh_varname,  nc%out_type, [nc%space_dimid, nc%name_dimid, nc%time_dimid], nc%vh_varid), "encounter_io_initialize nf90_def_var vh_varid"  )
+         call check( nf90_def_var(nc%id, nc%Gmass_varname, nc%out_type, [nc%name_dimid, nc%time_dimid], nc%Gmass_varid), "encounter_io_initialize nf90_def_var Gmass_varid"  )
          call check( nf90_def_var(nc%id, nc%loop_varname, NF90_INT, [nc%time_dimid], nc%loop_varid), "encounter_io_initialize nf90_def_var loop_varid"  )
          if (param%lclose) then
-            call check( nf90_def_var(nc%id, nc%radius_varname, nc%out_type, [nc%id_dimid, nc%time_dimid], nc%radius_varid), "encounter_io_initialize nf90_def_var radius_varid"  )
+            call check( nf90_def_var(nc%id, nc%radius_varname, nc%out_type, [nc%name_dimid, nc%time_dimid], nc%radius_varid), "encounter_io_initialize nf90_def_var radius_varid"  )
          end if
          if (param%lrotation) then
-            call check( nf90_def_var(nc%id, nc%Ip_varname, nc%out_type, [nc%space_dimid, nc%id_dimid, nc%time_dimid], nc%Ip_varid), "encounter_io_initialize nf90_def_var Ip_varid"  )
-            call check( nf90_def_var(nc%id, nc%rot_varname, nc%out_type, [nc%space_dimid, nc%id_dimid, nc%time_dimid], nc%rot_varid), "encounter_io_initialize nf90_def_var rot_varid"  )
+            call check( nf90_def_var(nc%id, nc%Ip_varname, nc%out_type, [nc%space_dimid, nc%name_dimid, nc%time_dimid], nc%Ip_varid), "encounter_io_initialize nf90_def_var Ip_varid"  )
+            call check( nf90_def_var(nc%id, nc%rot_varname, nc%out_type, [nc%space_dimid, nc%name_dimid, nc%time_dimid], nc%rot_varid), "encounter_io_initialize nf90_def_var rot_varid"  )
          end if
 
          call check( nf90_inquire(nc%id, nVariables=nvar), "encounter_io_initialize nf90_inquire nVariables"  )

src/fraggle/fraggle_io.f90

@@ -55,49 +55,48 @@ module subroutine fraggle_io_initialize_output(self, param)
             ! Dimensions
             call check( nf90_def_dim(nc%id, nc%event_dimname, nc%event_dimsize, nc%event_dimid), "fraggle_io_initialize nf90_def_dim event_dimid"  ) ! Dimension to store individual collision events
             call check( nf90_def_dim(nc%id, nc%space_dimname, NDIM,             nc%space_dimid), "fraggle_io_initialize nf90_def_dim space_dimid" )  ! 3D space dimension
-            call check( nf90_def_dim(nc%id, nc%id_dimname,    nc%id_dimsize,    nc%id_dimid),    "fraggle_io_initialize nf90_def_dim id_dimid" )     ! Dimension to store particle id numbers
+            call check( nf90_def_dim(nc%id, nc%name_dimname,  nc%name_dimsize,  nc%name_dimid),    "fraggle_io_initialize nf90_def_dim name_dimid" )     ! Dimension to store particle id numbers
             call check( nf90_def_dim(nc%id, nc%str_dimname,   NAMELEN,          nc%str_dimid),   "fraggle_io_initialize nf90_def_dim str_dimid"  )   ! Dimension for string variables (aka character arrays)
             call check( nf90_def_dim(nc%id, nc%stage_dimname, 2,                nc%stage_dimid), "fraggle_io_initialize nf90_def_dim stage_dimid"  ) ! Dimension for stage variables (aka "before" vs. "after"
 
             ! Dimension coordinates
             call check( nf90_def_var(nc%id, nc%space_dimname, NF90_CHAR,  nc%space_dimid, nc%space_varid), "fraggle_io_initialize nf90_def_var space_varid"  )
-            call check( nf90_def_var(nc%id, nc%id_dimname,    NF90_INT,   nc%id_dimid,    nc%id_varid),    "fraggle_io_initialize nf90_def_var id_varid"  )
-            call check( nf90_def_var(nc%id, nc%stage_dimname, NF90_CHAR,  [nc%str_dimid, nc%stage_dimid], nc%stage_varid), "fraggle_io_initialize nf90_def_var stage_varid"  )
+            call check( nf90_def_var(nc%id, nc%name_dimname,  NF90_CHAR, [nc%str_dimid, nc%name_dimid], nc%name_varid),   "fraggle_io_initialize nf90_def_var name_varid")
+            call check( nf90_def_var(nc%id, nc%stage_dimname, NF90_CHAR, [nc%str_dimid, nc%stage_dimid], nc%stage_varid), "fraggle_io_initialize nf90_def_var stage_varid"  )
 
             ! Variables
+            call check( nf90_def_var(nc%id, nc%id_varname,    NF90_INT,   nc%name_dimid,    nc%id_varid),    "fraggle_io_initialize nf90_def_var id_varid"  )
             call check( nf90_def_var(nc%id, nc%time_dimname,    nc%out_type, &
                                                                                  nc%event_dimid, nc%time_varid),    "fraggle_io_initialize nf90_def_var time_varid"  )
             call check( nf90_def_var(nc%id, nc%regime_varname,  NF90_CHAR,  &
                [nc%str_dimid,                                                    nc%event_dimid], nc%regime_varid), "fraggle_io_initialize nf90_def_var regime_varid")
             call check( nf90_def_var(nc%id, nc%Qloss_varname,  nc%out_type,  &
                [                                                                 nc%event_dimid], nc%Qloss_varid),  "fraggle_io_initialize nf90_def_var Qloss_varid")
-            call check( nf90_def_var(nc%id, nc%name_varname,    NF90_CHAR,  &
-               [nc%str_dimid,                   nc%id_dimid                                    ], nc%name_varid),   "fraggle_io_initialize nf90_def_var name_varid")
 
             call check( nf90_def_var(nc%id, nc%ptype_varname,   NF90_CHAR,  &
-               [nc%str_dimid,                   nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%ptype_varid),  "fraggle_io_initialize nf90_def_var ptype_varid")
+               [nc%str_dimid,                   nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%ptype_varid),  "fraggle_io_initialize nf90_def_var ptype_varid")
 
             call check( nf90_def_var(nc%id, nc%loop_varname,    NF90_INT, &
                [                                                                 nc%event_dimid], nc%loop_varid),   "fraggle_io_initialize nf90_def_var loop_varid")   
 
             call check( nf90_def_var(nc%id, nc%rh_varname,      nc%out_type,&
-               [              nc%space_dimid,   nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%rh_varid),     "fraggle_io_initialize nf90_def_var rh_varid")
+               [              nc%space_dimid,   nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%rh_varid),     "fraggle_io_initialize nf90_def_var rh_varid")
 
             call check( nf90_def_var(nc%id, nc%vh_varname,      nc%out_type,&
-               [              nc%space_dimid,   nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%vh_varid),     "fraggle_io_initialize nf90_def_var vh_varid")
+               [              nc%space_dimid,   nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%vh_varid),     "fraggle_io_initialize nf90_def_var vh_varid")
 
             call check( nf90_def_var(nc%id, nc%Gmass_varname,   nc%out_type,&
-               [                                nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%Gmass_varid),  "fraggle_io_initialize nf90_def_var Gmass_varid")
+               [                                nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%Gmass_varid),  "fraggle_io_initialize nf90_def_var Gmass_varid")
 
 
             call check( nf90_def_var(nc%id, nc%radius_varname,  nc%out_type,&
-               [                                nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%radius_varid), "fraggle_io_initialize nf90_def_var radius_varid")
+               [                                nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%radius_varid), "fraggle_io_initialize nf90_def_var radius_varid")
 
             call check( nf90_def_var(nc%id, nc%Ip_varname,      nc%out_type,&
-               [              nc%space_dimid,   nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%Ip_varid),     "fraggle_io_initialize nf90_def_var Ip_varid")
+               [              nc%space_dimid,   nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%Ip_varid),     "fraggle_io_initialize nf90_def_var Ip_varid")
 
             call check( nf90_def_var(nc%id, nc%rot_varname,     nc%out_type,&
-               [              nc%space_dimid,   nc%id_dimid,    nc%stage_dimid,  nc%event_dimid], nc%rot_varid),    "fraggle_io_initialize nf90_def_var rot_varid")
+               [              nc%space_dimid,   nc%name_dimid,    nc%stage_dimid,  nc%event_dimid], nc%rot_varid),    "fraggle_io_initialize nf90_def_var rot_varid")
 
             call check( nf90_def_var(nc%id, nc%ke_orb_varname,  nc%out_type,&
                [                                                nc%stage_dimid,  nc%event_dimid], nc%KE_orb_varid), "fraggle_io_initialize_output nf90_def_var KE_orb_varid")

src/modules/encounter_classes.f90

@@ -59,7 +59,7 @@ module encounter_classes
       character(NAMELEN) :: loop_varname = "loopnum" !! Loop number for encounter
       integer(I4B)       :: loop_varid               !! ID for the recursion level variable
       integer(I4B)       :: time_dimsize = 0         !! Number of time values in snapshot
-      integer(I4B)       :: id_dimsize   = 0         !! Number of potential id values in snapshot
+      integer(I4B)       :: name_dimsize   = 0         !! Number of potential id values in snapshot
       integer(I4B)       :: file_number  = 1         !! The number to append on the output file
    contains
       procedure :: initialize => encounter_io_initialize !! Initialize a set of parameters used to identify a NetCDF output object

src/modules/swiftest_classes.f90

@@ -34,9 +34,9 @@ module swiftest_classes
       character(NAMELEN) :: time_dimname            = "time"            !! name of the time dimension 
       integer(I4B)       :: time_dimid                                  !! ID for the time dimension 
       integer(I4B)       :: time_varid                                  !! ID for the time variable
-      character(NAMELEN) :: id_dimname              = "id"              !! name of the particle id dimension
-      integer(I4B)       :: id_dimid                                    !! ID for the particle id dimension
-      integer(I4B)       :: id_varid                                    !! ID for the particle name variable
+      character(NAMELEN) :: name_dimname            = "name"            !! name of the particle name dimension
+      integer(I4B)       :: name_dimid                                  !! ID for the particle name dimension
+      integer(I4B)       :: name_varid                                  !! ID for the particle name variable
       character(NAMELEN) :: space_dimname           = "space"           !! name of the space dimension
       integer(I4B)       :: space_dimid                                 !! ID for the space dimension
       integer(I4B)       :: space_varid                                 !! ID for the space variable
@@ -45,8 +45,8 @@ module swiftest_classes
       ! Non-dimension ids and variable names
       character(NAMELEN) :: ptype_varname           = "particle_type"   !! name of the particle type variable
       integer(I4B)       :: ptype_varid                                 !! ID for the particle type variable
-      character(NAMELEN) :: name_varname            = "name"            !! name of the particle name variable
-      integer(I4B)       :: name_varid                                  !! ID for the name variable 
+      character(NAMELEN) :: id_varname              = "id"              !! name of the particle id variable
+      integer(I4B)       :: id_varid                                    !! ID for the id variable 
       character(NAMELEN) :: npl_varname             = "npl"             !! name of the number of active massive bodies variable
       integer(I4B)       :: npl_varid                                   !! ID for the number of active massive bodies variable
       character(NAMELEN) :: ntp_varname             = "ntp"             !! name of the number of active test particles variable