Added some descriptions in Si LAMMPS tutorial.

docs/source/tutorial_pages/02_silicon_lammps.rst

@@ -1,8 +1,67 @@
 
 .. _label_tutorial_02:
 
+.. raw:: html
+
+    <style> .red {color:red} </style>
+
+.. role:: red
+
 Silicon with LAMMPS
 -------------------
 
-In this page, we show how to use ALAMODE together with the LAMMPS.
-As a simple example, we calculate phonon dispersion curves of Si using the Stillinger-Weber potential implemented in LAMMPS.
+Here, we demonstrate how to use ALAMODE together with LAMMPS.
+All input files can be found in the **example/Si_LAMMPS** directory.
+Before starting the tutorial, please build the LAMMPS code (e.g. ``lmp_serial``).
+
+As a simple example, we calculate phonon dispersion curves of Si using the Stillinger-Weber (SW) potential implemented in LAMMPS.
+First, you need to make two input files for LAMMPS: :red:`in.sw` and :red:`Si222.lammps` (file name is arbitrary, though).
+:red:`in.sw` is the main input file for LAMMPS, in which the type of the empirical force field is defined as follows:
+
+.. literalinclude:: ../../example/Si_LAMMPS/in.sw
+
+In the file :red:`Si222.lammps`, the lattice vectors and atomic positions of a relaxed supercell structure are defined as follows:
+
+.. literalinclude:: ../../example/Si_LAMMPS/Si222.lammps
+   :lines: 1-30
+
+Next, please generate a set of structure files for displaced configurations using 
+the python script::
+
+    $ python displace.py --LAMMPS=Si222.lammps --mag=0.01 --prefix harm  si222.pattern_HARMONIC
+    $ python displace.py --LAMMPS=Si222.lammps --mag=0.04 --prefix cubic si222.pattern_ANHARM3
+
+The pattern files can be generated by the **alm** code as decribed :ref:`here <tutorial_Si_step1>`.
+The above commands create ``harm1.lammps`` and ``cubic[01-20].lammps`` structure files.
+Then, run the following script and calculate atomic forces for the generated structures.
+This should finish in a few seconds.
+
+::
+
+    !#/bin/bash
+
+    cp harm1.lammps tmp.lammps
+    lmp_serial < in.sw > log.lammps
+    cp DISP DISP.harm1
+    cp FORCE FORCE.harm1
+
+    for ((i=1;i<=20;i++))
+    do
+        num=`echo $i | awk '{printf("%02d",$1)}'`
+        cp cubic${num}.lammps tmp.lammps
+        lmp_serial < in.sw > log.lammps
+        cp DISP DISP.cubic${num}
+        cp FORCE FORCE.cubic${num}
+    done
+
+After the force calculations are finished, displacement and force data sets 
+can be generated as follows::
+
+    $ python extract.py --LAMMPS=Si222.lammps --get=disp DISP.harm1 > disp.dat
+    $ python extract.py --LAMMPS=Si222.lammps --get=force FORCE.harm1 > force.dat
+
+    $ python extract.py --LAMMPS=Si222.lammps --get=disp DISP.cubic* > disp3.dat
+    $ python extract.py --LAMMPS=Si222.lammps --get=force FORCE.cubic* > force3.dat
+
+Then, using these files and following exactly the same procedure as the last tutorial section,
+you can calculate phonons and thermal conductivity of Si using the SW potential.