Fix bug in AvgChunkReader and add docs

doc/src/Python_formats.rst

@@ -0,0 +1,11 @@
+Output Readers
+==============
+
+.. py:module:: lammps.formats
+
+The Python package contains the :py:mod:`lammps.formats` module, which
+provides classes to post-process some of the output files generated by LAMMPS.
+
+.. automodule:: lammps.formats
+   :members:
+   :noindex:

doc/src/Python_head.rst

@@ -13,6 +13,7 @@ together.
    Python_module
    Python_ext
    Python_call
+   Python_formats
    Python_examples
    Python_error
    Python_trouble

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({

unittest/python/python-formats.py

@@ -73,7 +73,9 @@ class AvgChunkFiles(unittest.TestCase):
         self.assertEqual(cfile.timesteps, list(range(10000, 110000, 5000)))
 
         ntimesteps = len(cfile.timesteps)
+        ntotal_count = len(cfile.total_count)
         nchunks = len(cfile.chunks)
+        self.assertEqual(ntimesteps, ntotal_count)
         self.assertEqual(nchunks, 20)
 
         for i in range(1, nchunks+1):