Fixed problems identifiying the correct idslot to store bodies in the…

… various NetCDF files.

examples/Fragmentation/Fragmentation_Movie.py

@@ -143,7 +143,8 @@ def encounter_combiner(sim):
     ds = xr.combine_nested([data,enc],concat_dim='time').sortby("time").interpolate_na(dim="time")
 
     # Interpolate in time to make a smooth, constant time step dataset 
-    smooth_time = np.linspace(start=tgood.isel(time=0), stop=ds.time[-1], num=num_movie_frames)
+    # Add a bit of padding to the time, otherwise there are some issues with the interpolation in the last few frames.
+    smooth_time = np.linspace(start=tgood.isel(time=0), stop=ds.time[-1], num=int(1.2*num_movie_frames))
     ds = ds.interp(time=smooth_time)
 
     return ds
@@ -154,7 +155,6 @@ class AnimatedScatter(object):
     def __init__(self, sim, animfile, title, style, nskip=1):
 
         self.ds = encounter_combiner(sim)
-        nframes = int(self.ds['time'].size)
         self.sim = sim
         self.title = title
         self.body_color_list = {'Initial conditions': 'xkcd:windows blue',
@@ -168,7 +168,7 @@ def __init__(self, sim, animfile, title, style, nskip=1):
         self.fig, self.ax = self.setup_plot()
 
         # Then setup FuncAnimation.
-        self.ani = animation.FuncAnimation(self.fig, self.update_plot, interval=1, frames=range(0,nframes,nskip), blit=True)
+        self.ani = animation.FuncAnimation(self.fig, self.update_plot, interval=1, frames=range(0,num_movie_frames,nskip), blit=True)
         self.ani.save(animfile, fps=60, dpi=300, extra_args=['-vcodec', 'libx264'])
         print(f"Finished writing {animfile}")
 

src/collision/collision_io.f90

@@ -394,8 +394,11 @@ module subroutine collision_io_netcdf_write_frame_snapshot(self, history, param)
                      allocate(pl, source=after%pl)
                   end select
                   npl = pl%nbody
+
+                  ! This ensures that there first idslot will have the first body in it, not id 0 which is the default for a new idvals array
+                  if (.not.allocated(nc%idvals)) allocate(nc%idvals, source=pl%id)
                   do i = 1, npl
-                     idslot = findloc(history%idvals,pl%id(i),dim=1)
+                     call nc%find_idslot(pl%id(i), idslot) 
                      call netcdf_io_check( nf90_put_var(nc%id, nc%id_varid,     pl%id(i),     start=[   idslot              ]), "collision_io_netcdf_write_frame_snapshot nf90_put_var id_varid"  )
                      charstring = trim(adjustl(pl%info(i)%name))
                      call netcdf_io_check( nf90_put_var(nc%id, nc%name_varid,   charstring,   start=[1, idslot              ], count=[NAMELEN, 1]), "collision_io_netcdf_write_frame_snapshot nf90_put_var name_varid"  )

src/encounter/encounter_io.f90

@@ -248,8 +248,10 @@ module subroutine encounter_io_netcdf_write_frame_snapshot(self, history, param)
             call netcdf_io_check( nf90_put_var(nc%id, nc%time_varid, self%t, start=[tslot]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var time_varid"  )
 
             npl = pl%nbody
+            ! This ensures that there first idslot will have the first body in it, not id 0 which is the default for a new idvals array
+            if (.not.allocated(nc%idvals)) allocate(nc%idvals, source=pl%id)
             do i = 1, npl
-               idslot = findloc(history%idvals,pl%id(i),dim=1)
+               call nc%find_idslot(pl%id(i), idslot) 
                call netcdf_io_check( nf90_put_var(nc%id, nc%id_varid, pl%id(i),   start=[idslot]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl id_varid"  )
                call netcdf_io_check( nf90_put_var(nc%id, nc%rh_varid, pl%rh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl rh_varid"  )
                call netcdf_io_check( nf90_put_var(nc%id, nc%vh_varid, pl%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var pl vh_varid"  )
@@ -269,8 +271,9 @@ module subroutine encounter_io_netcdf_write_frame_snapshot(self, history, param)
             end do
 
             ntp = tp%nbody
+            if (.not.allocated(nc%idvals)) allocate(nc%idvals, source=tp%id)
             do i = 1, ntp
-               idslot = findloc(history%idvals,tp%id(i),dim=1)
+               call nc%find_idslot(tp%id(i), idslot) 
                call netcdf_io_check( nf90_put_var(nc%id, nc%id_varid, tp%id(i), start=[idslot]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp id_varid"  )
                call netcdf_io_check( nf90_put_var(nc%id, nc%rh_varid, tp%rh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp rh_varid"  )
                call netcdf_io_check( nf90_put_var(nc%id, nc%vh_varid, tp%vh(:,i), start=[1,idslot,tslot], count=[NDIM,1,1]), "encounter_io_netcdf_write_frame_snapshot nf90_put_var tp vh_varid"  )

src/encounter/encounter_util.f90

@@ -248,7 +248,7 @@ module subroutine encounter_util_get_vals_storage(self, idvals, tvals)
 
          allocate(idvals(ntotal))
          nlo = 1
-         ! Second pass to store all ids get all of the ids stored
+         ! Second pass to get all of the ids stored
          do i = 1, nsnaps
             if (allocated(self%frame(i)%item)) then
                select type(snapshot => self%frame(i)%item)

src/netcdf_io/netcdf_io_implementations.f90

@@ -47,7 +47,7 @@ module subroutine netcdf_io_close(self)
    end subroutine netcdf_io_close
 
 
-   module subroutine netcdf_io_find_tslot(self, t)
+   module subroutine netcdf_io_find_tslot(self, t, tslot)
       !! author: David A. Minton
       !! 
       !! Given an open NetCDF file and a value of time t, finds the index of the time value (aka the time slot) to place a new set of data.
@@ -56,12 +56,13 @@ module subroutine netcdf_io_find_tslot(self, t)
       ! Arguments
       class(netcdf_parameters), intent(inout) :: self  !! Parameters used to identify a particular NetCDF dataset
       real(DP),                 intent(in)    :: t     !! The value of time to search for
+      integer(I4B),             intent(out)   :: tslot !! The index of the time slot where this data belongs
       ! Internals
       real(DP), dimension(:), allocatable :: tvals
 
-      self%tslot = 0
 
       if (.not.self%lfile_is_open) return
+      tslot = 0
 
       call netcdf_io_check( nf90_inquire_dimension(self%id, self%time_dimid, self%time_dimname, len=self%max_tslot), "netcdf_io_find_tslot nf90_inquire_dimension max_tslot"  )
       if (self%max_tslot > 0) then
@@ -72,19 +73,54 @@ module subroutine netcdf_io_find_tslot(self, t)
          tvals(1) = -huge(1.0_DP)
       end if
 
-      self%tslot = findloc(tvals, t, dim=1)
-      if (self%tslot == 0) self%tslot = self%max_tslot + 1
-      self%max_tslot = max(self%max_tslot, self%tslot)
+      tslot = findloc(tvals, t, dim=1)
+      if (tslot == 0) tslot = self%max_tslot + 1
+      self%max_tslot = max(self%max_tslot, tslot)
+      self%tslot = tslot
 
       return
    end subroutine netcdf_io_find_tslot
 
 
-   module subroutine netcdf_io_get_idvals(self)
+   module subroutine netcdf_io_find_idslot(self, id, idslot)
       !! author: David A. Minton
       !! 
       !! Given an open NetCDF file and a value of id, finds the index of the id value (aka the id slot) to place a new set of data.
-      !! The returned value of idslot will correspond to the first index value where the value of id is equal to a saved id value. If none are found, it is the next available index.
+      !! The returned value of idslot will correspond to the first index value where the value of id is greater than or equal to the saved id value.
+      implicit none
+      ! Arguments
+      class(netcdf_parameters), intent(inout) :: self   !! Parameters used to identify a particular NetCDF dataset
+      integer(I4B),             intent(in)    :: id     !! The value of id to search for
+      integer(I4B),             intent(out)   :: idslot !! The index of the id slot where this data belongs
+      ! Internals
+      integer(I4B), dimension(:), allocatable :: idvals
+
+      if (.not.self%lfile_is_open) return
+
+      if (.not.allocated(self%idvals)) call self%get_idvals()
+      self%max_idslot = size(self%idvals)
+      idslot = findloc(self%idvals, id, dim=1)
+      if (idslot == 0) then
+         self%max_idslot = self%max_idslot + 1
+         idslot = self%max_idslot
+
+         ! Update the idvals array
+         allocate(idvals(idslot))
+         idvals(1:idslot-1) = self%idvals(1:idslot-1)
+         idvals(idslot) = id
+         call move_alloc(idvals, self%idvals) 
+      end if
+
+      self%idslot = idslot
+
+      return
+   end subroutine netcdf_io_find_idslot
+
+
+   module subroutine netcdf_io_get_idvals(self)
+      !! author: David A. Minton
+      !! 
+      !! Gets a full list of id values 
       implicit none
       ! Arguments
       class(netcdf_parameters),                            intent(inout) :: self   !! Parameters used to identify a particular NetCDF dataset
@@ -99,7 +135,7 @@ module subroutine netcdf_io_get_idvals(self)
          call netcdf_io_check( nf90_get_var(self%id, self%id_varid, self%idvals(:), start=[1]), "netcdf_io_find_idslot get_var"  )
       else
          allocate(self%idvals(1))
-         self%idvals(1) = -huge(1)
+         self%idvals(1) = 0
       end if
 
       return

src/netcdf_io/netcdf_io_module.f90

@@ -27,6 +27,7 @@ module netcdf_io
       integer(I4B)       :: tslot                   = 1                 !! The current time slot that gets passed to the NetCDF reader/writer
       integer(I4B)       :: max_tslot               = 0                 !! Records the last index value of time in the NetCDF file
       integer(I4B), dimension(:), allocatable :: idvals                 !! Array of id values in this NetCDF file
+      integer(I4B)       :: idslot                  = 1                 !! The current id slot that gets passed to the NetCDF reader/writer
       integer(I4B)       :: max_idslot              = 0                 !! Records the last index value of id in the NetCDF file
 
       ! Dimension ids and variable names
@@ -142,10 +143,11 @@ module netcdf_io
       integer(I4B)       :: discard_body_id_varid                       !! ID for the id of the other body involved in the discard
       logical            :: lpseudo_vel_exists = .false.                !! Logical flag to indicate whether or not the pseudovelocity vectors were present in an old file.
    contains
-      procedure :: close      => netcdf_io_close       !! Closes an open NetCDF file
-      procedure :: find_tslot => netcdf_io_find_tslot  !! Finds the time dimension index for a given value of t
-      procedure :: get_idvals => netcdf_io_get_idvals  !! Gets the valid id numbers currently stored in this dataset
-      procedure :: sync       => netcdf_io_sync        !! Syncrhonize the disk and memory buffer of the NetCDF file (e.g. commit the frame files stored in memory to disk) 
+      procedure :: close       => netcdf_io_close       !! Closes an open NetCDF file
+      procedure :: find_tslot  => netcdf_io_find_tslot  !! Finds the time dimension index for a given value of t
+      procedure :: find_idslot => netcdf_io_find_idslot !! Finds the id dimension index for a given value of id
+      procedure :: get_idvals  => netcdf_io_get_idvals  !! Gets the valid id numbers currently stored in this dataset
+      procedure :: sync        => netcdf_io_sync        !! Syncrhonize the disk and memory buffer of the NetCDF file (e.g. commit the frame files stored in memory to disk) 
    end type netcdf_parameters
 
    interface
@@ -165,11 +167,19 @@ module subroutine netcdf_io_get_idvals(self)
          class(netcdf_parameters),                            intent(inout) :: self   !! Parameters used to identify a particular NetCDF dataset
       end subroutine netcdf_io_get_idvals
 
-      module subroutine netcdf_io_find_tslot(self, t)
+      module subroutine netcdf_io_find_tslot(self, t, tslot)
          implicit none
          class(netcdf_parameters), intent(inout) :: self  !! Parameters used to identify a particular NetCDF dataset
          real(DP),                 intent(in)    :: t     !! The value of time to search for
+         integer(I4B),             intent(out)   :: tslot !! The index of the time slot where this data belongs
       end subroutine netcdf_io_find_tslot
+
+      module subroutine netcdf_io_find_idslot(self, id, idslot)
+         implicit none
+         class(netcdf_parameters), intent(inout) :: self   !! Parameters used to identify a particular NetCDF dataset
+         integer(I4B),             intent(in)    :: id     !! The value of id to search for
+         integer(I4B),             intent(out)   :: idslot !! The index of the id slot where this data belongs
+      end subroutine netcdf_io_find_idslot
 
       module subroutine netcdf_io_sync(self)
          implicit none