add the decription of output file

Author: luowh35

doc/gpumd/input_parameters/compute_chunk.rst

@@ -106,18 +106,39 @@ Output file
 -----------
 
 The results are written to ``compute_chunk.out``.
-For each output time, there is one line per chunk with the following format::
+The file is appended to if it already exists.
+For each output time, there are :math:`N_\text{chunk}` consecutive lines (one per chunk), with the following format per line::
 
   <chunk_id> <coord1> [<coord2>] [<coord3>] <avg_count> <value1> [<value2>] ...
 
-where:
+The columns are:
 
-* :attr:`chunk_id` is the zero-based index of the chunk.
-* :attr:`coord1` (and :attr:`coord2`, :attr:`coord3` for 2D/3D binning) are the center coordinates of the chunk in Ångströms.
-* :attr:`avg_count` is the time-averaged number of atoms in the chunk.
-* :attr:`value1`, :attr:`value2`, ... are the time-averaged values of the requested quantities, in the order they were specified in the command.
+* :attr:`chunk_id`: the zero-based index of the chunk (dimensionless integer).
+* :attr:`coord1` (and :attr:`coord2`, :attr:`coord3` for 2D/3D binning): the center coordinates (in units of Å) of the chunk along the corresponding binning axis.
+* :attr:`avg_count`: the time-averaged number of atoms in the chunk (dimensionless).
+* :attr:`value1`, :attr:`value2`, ...: the time-averaged values of the requested quantities, in the same order as specified in the command. The units for each quantity are:
 
-Output blocks for successive time points are separated by blank lines.
+  - :attr:`temperature`: K
+  - :attr:`density/number`: Å\ :sup:`-3` (number of atoms per volume)
+  - :attr:`density/mass`: amu/Å\ :sup:`3` (total atomic mass per volume)
+  - :attr:`vx`, :attr:`vy`, :attr:`vz`: Å/fs
+  - :attr:`fx`, :attr:`fy`, :attr:`fz`: eV/Å
+
+The temperature is computed from the kinetic energy of the atoms in each chunk as :math:`T = 2 E_\text{k} / (3 k_\text{B} N)`, where :math:`E_\text{k}` is the total kinetic energy, :math:`N` is the atom count, and :math:`k_\text{B}` is the Boltzmann constant.
+The velocity and force values are per-atom averages within each chunk.
+
+For example, the command::
+
+  compute_chunk 10 100 bin/1d z lower 2.0 temperature density/number
+
+produces output lines of the form::
+
+  0 1.000000 52.0 3.0012345678e+02 2.5000000000e-02
+  1 3.000000 48.0 2.9876543210e+02 2.4000000000e-02
+  ...
+
+Here, each line contains: chunk index, bin center along z (Å), average atom count, temperature (K), and number density (Å\ :sup:`-3`).
+The output blocks for successive time points are written consecutively with no blank line separator; each block contains exactly :math:`N_\text{chunk}` lines.
 
 
 Caveats