Getting the collision ouput data cleaned up.

examples/Fragmentation/Fragmentation_Movie.py

@@ -203,7 +203,7 @@ 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, collision_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.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)

python/swiftest/swiftest/simulation_class.py

@@ -2958,8 +2958,8 @@ def clean(self):
                      ]
         glob_files = [self.simdir.glob("**/dump_param?.in")] \
                      + [self.simdir.glob("**/dump_bin?.nc")] \
-                     + [self.simdir.glob("**/enc*.nc")] \
-                     + [self.simdir.glob("**/frag*.nc")]
+                     + [self.simdir.glob("**/encounter_*.nc")] \
+                     + [self.simdir.glob("**/collision_*.nc")]
 
         for f in old_files:
             if f.exists():

src/encounter/encounter_io.f90

@@ -60,7 +60,6 @@ module subroutine encounter_io_initialize(self, param)
       logical :: fileExists
       character(len=STRMAX) :: errmsg
       integer(I4B) :: ndims, i
-      character(len=NAMELEN) :: charstring
 
       associate(nc => self)
          dfill = ieee_value(dfill, IEEE_QUIET_NAN)
@@ -153,7 +152,7 @@ module subroutine encounter_io_write_frame(self, nc, param)
       class(swiftest_parameters),     intent(inout) :: param !! Current run configuration parameters
       ! Internals
       integer(I4B)           :: i, tslot, idslot, old_mode, npl, ntp
-      character(len=NAMELEN) :: charstring
+      character(len=:), allocatable :: charstring
 
       tslot = param%ioutput
       associate(pl => self%pl, tp => self%tp)
@@ -179,9 +178,9 @@ module subroutine encounter_io_write_frame(self, nc, param)
             end if
 
             charstring = trim(adjustl(pl%info(i)%name))
-            call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_write_frame nf90_put_var pl name_varid"  )
+            call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_write_frame nf90_put_var pl name_varid"  )
             charstring = trim(adjustl(pl%info(i)%particle_type))
-            call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_write_frame nf90_put_var pl particle_type_varid"  )
+            call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_write_frame nf90_put_var pl particle_type_varid"  )
          end do
 
          ntp = tp%nbody
@@ -192,9 +191,9 @@ module subroutine encounter_io_write_frame(self, nc, param)
             call check( nf90_put_var(nc%id, nc%vh_varid, tp%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "encounter_io_write_frame nf90_put_var tp vh_varid"  )
 
             charstring = trim(adjustl(tp%info(i)%name))
-            call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_write_frame nf90_put_var tp name_varid"  )
+            call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_write_frame nf90_put_var tp name_varid"  )
             charstring = trim(adjustl(tp%info(i)%particle_type))
-            call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "encounter_io_write_frame nf90_put_var tp particle_type_varid"  )
+            call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "encounter_io_write_frame nf90_put_var tp particle_type_varid"  )
          end do
 
          call check( nf90_set_fill(nc%id, old_mode, old_mode) )

src/fraggle/fraggle_io.f90

@@ -61,7 +61,7 @@ module subroutine fraggle_io_initialize_output(self, param)
          ! 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%stage_dimid, nc%stage_varid), "fraggle_io_initialize nf90_def_var stage_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%time_dimname,    nc%out_type, &
@@ -134,7 +134,8 @@ module subroutine fraggle_io_initialize_output(self, param)
 
          ! Add in the space and stage dimension coordinates
          call check( nf90_put_var(nc%id, nc%space_varid, nc%space_coords, start=[1], count=[NDIM]), "fraggle_io_initialize nf90_put_var space"  )
-         call check( nf90_put_var(nc%id, nc%stage_varid, nc%stage_coords, start=[1], count=[2]), "fraggle_io_initialize nf90_put_var stage"  )
+         call check( nf90_put_var(nc%id, nc%stage_varid, nc%stage_coords(1), start=[1,1], count=[len(nc%stage_coords(1)),1]), "fraggle_io_initialize nf90_put_var stage 1"  )
+         call check( nf90_put_var(nc%id, nc%stage_varid, nc%stage_coords(2), start=[1,2], count=[len(nc%stage_coords(2)),1]), "fraggle_io_initialize nf90_put_var stage 2"  )
 
          ! Pre-fill id slots with ids
          call check( nf90_put_var(nc%id, nc%id_varid, [(-1,i=1,param%maxid)], start=[1], count=[param%maxid]), "fraggle_io_initialize nf90_put_varid_varid"  )
@@ -160,7 +161,7 @@ module subroutine fraggle_io_write_frame(self, nc, param)
       class(swiftest_parameters),        intent(inout) :: param  !! Current run configuration parameters
       ! Internals
       integer(I4B)           :: i, eslot, idslot, old_mode, npl
-      character(len=NAMELEN) :: charstring
+      character(len=:), allocatable :: charstring
 
       eslot = param%ioutput
       associate(pl => self%colliders%pl, colliders => self%colliders, fragments => self%fragments)
@@ -178,9 +179,9 @@ module subroutine fraggle_io_write_frame(self, nc, param)
                idslot = pl%id(i)
                call check( nf90_put_var(nc%id, nc%id_varid,     pl%id(i),     start=[   idslot         ]), "fraggle_io_write_frame nf90_put_var id_varid"  )
                charstring = trim(adjustl(pl%info(i)%name))
-               call check( nf90_put_var(nc%id, nc%name_varid,   charstring,   start=[1, idslot], count=[NAMELEN, 1]), "fraggle_io_write_frame nf90_put_var name_varid"  )
+               call check( nf90_put_var(nc%id, nc%name_varid,   charstring,   start=[1, idslot], count=[len(charstring), 1]), "fraggle_io_write_frame nf90_put_var name_varid"  )
                charstring = trim(adjustl(pl%info(i)%particle_type))
-               call check( nf90_put_var(nc%id, nc%ptype_varid,  charstring,   start=[1, idslot,    eslot], count=[NAMELEN, 1, 1]), "fraggle_io_write_frame nf90_put_var particle_type_varid"  )
+               call check( nf90_put_var(nc%id, nc%ptype_varid,  charstring,   start=[1, idslot,    eslot], count=[len(charstring), 1, 1]), "fraggle_io_write_frame nf90_put_var particle_type_varid"  )
 
                call check( nf90_put_var(nc%id, nc%rh_varid,     pl%rh(:,i),   start=[1, idslot, 1, eslot], count=[NDIM,1,1,1]), "fraggle_io_write_frame nf90_put_var rh_varid"  )
                call check( nf90_put_var(nc%id, nc%vh_varid,     pl%vh(:,i),   start=[1, idslot, 1, eslot], count=[NDIM,1,1,1]), "fraggle_io_write_frame nf90_put_var vh_varid"  )

src/modules/fraggle_classes.f90

@@ -116,7 +116,7 @@ module fraggle_classes
       integer(I4B)       :: stage_dimid                                     !! ID for the stage dimension
       integer(I4B)       :: stage_varid                                     !! ID for the stage variable  
       character(NAMELEN) :: stage_dimname            = "stage"              !! name of the stage dimension (before/after)
-      character(len=6), dimension(2) :: stage_coords = ["before", "after "] !! The stage coordinate labels
+      character(len=6), dimension(2) :: stage_coords = ["before", "after"] !! The stage coordinate labels
 
       character(NAMELEN) :: event_dimname = "collision" !! Name of collision event dimension
       integer(I4B)       :: event_dimid                 !! ID for the collision event dimension       

src/netcdf/netcdf.f90

@@ -1163,7 +1163,7 @@ module subroutine netcdf_write_info_base(self, nc, param)
       ! Internals
       integer(I4B)                              :: i, j, idslot, old_mode
       integer(I4B), dimension(:), allocatable   :: ind
-      character(len=NAMELEN)                    :: charstring
+      character(len=:), allocatable             :: charstring
 
       ! This string of spaces of length NAMELEN is used to clear out any old data left behind inside the string variables
       call check( nf90_set_fill(nc%id, nf90_nofill, old_mode), "netcdf_write_info_base nf90_set_fill nf90_nofill"  )
@@ -1180,14 +1180,14 @@ module subroutine netcdf_write_info_base(self, nc, param)
                call check( nf90_put_var(nc%id, nc%id_varid, self%id(j), start=[idslot]), "netcdf_write_info_base nf90_put_var id_varid"  )
 
                charstring = trim(adjustl(self%info(j)%name))
-               call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_write_info_base nf90_put_var name_varid"  )
+               call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_write_info_base nf90_put_var name_varid"  )
 
                charstring = trim(adjustl(self%info(j)%particle_type))
-               call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_write_info_base nf90_put_var particle_type_varid"  )
+               call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_write_info_base nf90_put_var particle_type_varid"  )
 
                if (param%lclose) then
                   charstring = trim(adjustl(self%info(j)%origin_type))
-                  call check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_write_info_base nf90_put_var origin_type_varid"  )
+                  call check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_write_info_base nf90_put_var origin_type_varid"  )
                   call check( nf90_put_var(nc%id, nc%origin_time_varid,  self%info(j)%origin_time,  start=[idslot]), "netcdf_write_info_base nf90_put_var origin_time_varid"  )
                   call check( nf90_put_var(nc%id, nc%origin_rh_varid,    self%info(j)%origin_rh(:), start=[1,idslot], count=[NDIM,1]), "netcdf_write_info_base nf90_put_var origin_rh_varid"  )
                   call check( nf90_put_var(nc%id, nc%origin_vh_varid,    self%info(j)%origin_vh(:), start=[1,idslot], count=[NDIM,1]), "netcdf_write_info_base nf90_put_var origin_vh_varid"  )
@@ -1206,14 +1206,14 @@ module subroutine netcdf_write_info_base(self, nc, param)
          call check( nf90_put_var(nc%id, nc%id_varid, self%id, start=[idslot]), "netcdf_write_info_base nf90_put_var cb id_varid"  )
 
          charstring = trim(adjustl(self%info%name))
-         call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_write_info_base nf90_put_var cb name_varid"  )
+         call check( nf90_put_var(nc%id, nc%name_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_write_info_base nf90_put_var cb name_varid"  )
 
          charstring = trim(adjustl(self%info%particle_type))
-         call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_write_info_base nf90_put_var cb ptype_varid"  )
+         call check( nf90_put_var(nc%id, nc%ptype_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_write_info_base nf90_put_var cb ptype_varid"  )
 
          if (param%lclose) then
             charstring = trim(adjustl(self%info%origin_type))
-            call check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[NAMELEN, 1]), "netcdf_write_info_base nf90_put_var cb origin_type_varid"  )
+            call check( nf90_put_var(nc%id, nc%origin_type_varid, charstring, start=[1, idslot], count=[len(charstring), 1]), "netcdf_write_info_base nf90_put_var cb origin_type_varid"  )
 
             call check( nf90_put_var(nc%id, nc%origin_time_varid, self%info%origin_time, start=[idslot]), "netcdf_write_info_base nf90_put_var cb origin_time_varid"  )
             call check( nf90_put_var(nc%id, nc%origin_rh_varid, self%info%origin_rh(:), start=[1, idslot], count=[NDIM,1]), "netcdf_write_info_base nf90_put_var cb origin_rh_varid"  )

src/symba/symba_io.f90

@@ -21,27 +21,30 @@ module subroutine symba_io_dump_encounter(self, param)
       class(symba_nbody_system),  intent(inout) :: self  !! SyMBA nbody system object
       class(symba_parameters),    intent(inout) :: param !! Current run configuration parameters 
 
-      if (self%encounter_history%iframe == 0) return ! No enounters in this interval
 
       associate(encounter_history => self%encounter_history, nce => self%encounter_history%nc, eframe => self%encounter_history%iframe,&
                 collision_history => self%collision_history, ncc => self%collision_history%nc, cframe => self%collision_history%iframe)
 
-         ! Create and save the output files for this encounter and fragmentation
-         nce%file_number = nce%file_number + 1 
-         nce%time_dimsize = maxval(encounter_history%tslot(:))
-         write(nce%file_name, '("encounter_",I0.6,".nc")') nce%file_number
-         call nce%initialize(param)
-         call encounter_history%dump(param)
-         call nce%close()
-         call encounter_history%reset()
-
-         ncc%file_number = ncc%file_number + 1 
-         write(ncc%file_name, '("collision_",I0.6,".nc")') ncc%file_number
-         ncc%time_dimsize = maxval(collision_history%tslot(:))
-         call ncc%initialize(param)
-         call collision_history%dump(param)
-         call ncc%close()
-         call collision_history%reset()
+         if (encounter_history%iframe > 0) then
+            ! Create and save the output files for this encounter and fragmentation
+            nce%file_number = nce%file_number + 1 
+            nce%time_dimsize = maxval(encounter_history%tslot(:))
+            write(nce%file_name, '("encounter_",I0.6,".nc")') nce%file_number
+            call nce%initialize(param)
+            call encounter_history%dump(param)
+            call nce%close()
+            call encounter_history%reset()
+         end if
+
+         if (collision_history%iframe > 0) then
+            ncc%file_number = ncc%file_number + 1 
+            write(ncc%file_name, '("collision_",I0.6,".nc")') ncc%file_number
+            ncc%time_dimsize = maxval(collision_history%tslot(:))
+            call ncc%initialize(param)
+            call collision_history%dump(param)
+            call ncc%close()
+            call collision_history%reset()
+         end if
       end associate
 
       return