Fix PHEW empty clumps

csiborgtools/read/readsim.py

@@ -16,7 +16,7 @@
 Functions to read in the particle and clump files.
 """
 from abc import ABC, abstractmethod
-from os.path import isfile, join
+from os.path import isfile, join, getsize
 from warnings import warn
 
 import numpy
@@ -329,10 +329,15 @@ class CSiBORGReader(BaseReader):
         fname = join(self.paths.snapshots(nsim, "csiborg", tonew=False),
                      "output_{}".format(nsnap),
                      "clump_{}.dat".format(nsnap))
-        if not isfile(fname):
-            raise FileExistsError("Clump file `{}` does not exist."
-                                  .format(fname))
+
+        if not isfile(fname) or getsize(fname) == 0:
+            raise FileExistsError(f"Clump file `{fname}` does not exist.")
+
         data = numpy.genfromtxt(fname)
+
+        if data.ndim == 1:
+            raise FileExistsError(f"Invalid clump file `{fname}`.")
+
         # How the data is stored in the clump file.
         clump_cols = {"index": (0, numpy.int32),
                       "level": (1, numpy.int32),

scripts/sort_initsnap.py

@@ -327,8 +327,12 @@ def make_phew_halo_catalogue(nsim, find_ultimate_parent, verbose):
         f.close()
 
     for nsnap in tqdm(snapshots, disable=not verbose, desc="Snapshot"):
-        data = reader.read_phew_clumps(nsnap, nsim, find_ultimate_parent=False,
-                                       verbose=False)
+        try:
+            data = reader.read_phew_clumps(
+                nsnap, nsim, find_ultimate_parent=find_ultimate_parent,
+                verbose=False)
+        except FileExistsError:
+            continue
 
         with h5py.File(fname, "r+") as f:
             grp = f.create_group(str(nsnap))
@@ -364,7 +368,7 @@ def main(nsim, args):
         calculate_initial(nsim, args.simname, args.halofinder, True)
 
     if args.make_phew:
-        make_phew_halo_catalogue(nsim, True, True)
+        make_phew_halo_catalogue(nsim, False, True)
 
 
 if __name__ == "__main__":