Fix bug in AvgChunkReader and add docs

python/lammps/formats.py

@@ -12,13 +12,25 @@
 # -------------------------------------------------------------------------
 
 ################################################################################
-# LAMMPS data formats
+# LAMMPS output formats
 # Written by Richard Berger <richard.berger@temple.edu>
 ################################################################################
 
 import re
 
 class LogFile:
+  """Reads LAMMPS log files and extracts the thermo information
+
+  It supports both the default thermo output style (including custom) and multi.
+
+  :param filename: path to log file
+  :type  filename: str
+
+  :ivar runs: List of LAMMPS runs in log file. Each run is a dictionary with
+              thermo fields as keys, storing the values over time
+  :ivar errors: List of error lines in log file
+  """
+
   STYLE_DEFAULT = 0
   STYLE_MULTI   = 1
 
@@ -73,7 +85,17 @@ class LogFile:
                         else:
                             current_run[k].append(float(v))
 
+
 class AvgChunkFile:
+  """Reads files generated by fix ave/chunk
+
+  :param filename: path to ave/chunk file
+  :type  filename: str
+
+  :ivar timesteps: List of timesteps stored in file
+  :ivar total_count: total count over time
+  :ivar chunks: List of chunks. Each chunk is a dictionary containing its ID, the coordinates, and the averaged quantities
+  """
   def __init__(self, filename):
     with open(filename, 'rt') as f:
       timestep = None
@@ -121,6 +143,7 @@ class AvgChunkFile:
           total_count = float(parts[2])
 
           self.timesteps.append(timestep)
+          self.total_count.append(total_count)
 
           for i in range(num_chunks):
             self.chunks.append({