The encounter output files are now merged properly into the .enc inst…

…ance variable

examples/Fragmentation/Fragmentation_Movie.py

@@ -84,7 +84,8 @@ class AnimatedScatter(object):
     """An animated scatter plot using matplotlib.animations.FuncAnimation."""
 
     def __init__(self, sim, animfile, title, nskip=1):
-        self.ds = sim.enc.mean(dim="encounter") # Reduce out the encounter dimension
+        tgood = sim.enc.where(sim.enc['Gmass'] > 9e-8).time
+        self.ds = sim.enc.sel(time=tgood)
         nframes = int(self.ds['time'].size)
         self.sim = sim
         self.title = title
@@ -109,8 +110,8 @@ def setup_plot(self):
 
         # Calculate the distance along the y-axis between the colliding bodies at the start of the simulation.
         # This will be used to scale the axis limits on the movie.
-        rhy1 = self.ds['rh'].isel(time=0).sel(name="Body1",space='y').values[()]
-        rhy2 = self.ds['rh'].isel(time=0).sel(name="Body2",space='y').values[()]
+        rhy1 = self.ds['rh'].sel(name="Body1",space='y').isel(time=0).values[()]
+        rhy2 = self.ds['rh'].sel(name="Body2",space='y').isel(time=0).values[()]
 
         scale_frame =   abs(rhy1) + abs(rhy2)
         ax = plt.Axes(fig, [0.1, 0.1, 0.8, 0.8])
@@ -133,12 +134,13 @@ def center(Gmass, x, y):
             x = x[~np.isnan(x)]
             y = y[~np.isnan(y)]
             Gmass = Gmass[~np.isnan(Gmass)]
+            x = x[Gmass]
             x_com = np.sum(Gmass * x) / np.sum(Gmass)
-            y_com = np.sum(Gmass * y) / np.sum(Gmass)
+            y_com = #np.sum(Gmass * y) / np.sum(Gmass)
             return x_com, y_com
 
         Gmass, rh, point_rad = next(self.data_stream(frame))
-        x_com, y_com = center(Gmass, rh[:,0], rh[:,1])
+        #x_com, y_com = center(Gmass, rh[:,0], rh[:,1])
         self.scatter_artist.set_offsets(np.c_[rh[:,0] - x_com, rh[:,1] - y_com])
         self.scatter_artist.set_sizes(point_rad**2)
         return self.scatter_artist,

python/swiftest/swiftest/simulation_class.py

@@ -2770,7 +2770,7 @@ def _preprocess(ds, param):
             return io.process_netcdf_input(ds,param)
         partial_func = partial(_preprocess, param=self.param)
 
-        self.enc = xr.open_mfdataset(enc_files,parallel=True,combine="nested", concat_dim="encounter",preprocess=partial_func)
+        self.enc = xr.open_mfdataset(enc_files,parallel=True,preprocess=partial_func,mask_and_scale=True)
         self.enc = io.process_netcdf_input(self.enc, self.param)
 
         return

src/symba/symba_io.f90

@@ -137,7 +137,7 @@ end subroutine symba_io_encounter_initialize_output
    module subroutine symba_io_encounter_write_frame(self, nc, param)
       !! author: David A. Minton
       !!
-      !! Write a frame of output of an encounter list structure.
+      !! Write a frame of output of an encounter trajectory.
       use netcdf
       implicit none
       ! Arguments
@@ -369,7 +369,7 @@ module subroutine symba_io_start_encounter(self, param, t)
       call self%encounter_history%reset()
 
       ! Empty out the time slot array for the next pass
-      self%encounter_history%tvals(:) = -huge(1.0_DP)
+      self%encounter_history%tvals(:) = huge(1.0_DP)
 
       ! Take the snapshot at the start of the encounter
       call self%snapshot(param, t) 

src/symba/symba_util.f90

@@ -1313,7 +1313,7 @@ module subroutine symba_util_take_encounter_snapshot(self, param, t)
       !! author: David A. Minton
       !!
       !! Takes a minimal snapshot of the state of the system during an encounter so that the trajectories
-      !! Can be played back through the encounter
+      !! can be played back through the encounter
       implicit none
       ! Internals
       class(symba_nbody_system),  intent(inout) :: self  !! SyMBA nbody system object
@@ -1401,7 +1401,7 @@ module subroutine symba_util_take_encounter_snapshot(self, param, t)
                ! Find out which time slot this belongs in by searching for an existing slot
                ! with the same value of time or the first available one
                do i = 1, self%encounter_history%nframes
-                  if (t >= self%encounter_history%tvals(i)) then
+                  if (t <= self%encounter_history%tvals(i)) then
                      snapshot%tslot = i
                      self%encounter_history%tvals(i) = t
                      exit