Update figures in tutorial

ttadano · Oct 31, 2017 · b7cc3f9 · b7cc3f9
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Showing 8 changed files with 12 additions and 23 deletions.
diff --git a/docs/img/Si_phband_DFT.png b/docs/img/Si_phband_DFT.png
diff --git a/docs/img/Si_phdos_DFT.png b/docs/img/Si_phdos_DFT.png
diff --git a/docs/img/si_phband.png b/docs/img/si_phband.png
diff --git a/docs/img/si_phdos.png b/docs/img/si_phdos.png
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -136,7 +136,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied

diff --git a/docs/source/tutorial_pages/01_silicon.rst b/docs/source/tutorial_pages/01_silicon.rst
@@ -81,12 +81,6 @@ Using the script :red:`displace.py` in the tools/ directory, you can generate th
 
         $ python displace.py --xTAPP=si222.cg --mag=0.02 si222.pattern_HARMONIC
 
-    **LAMMPS**
-    ::
-
-        $ python displace.py --LAMMPS=si222.lammps --mag=0.02 si222.pattern_HARMONIC
-
-
 The ``--mag`` option specifies the displacement length in units of Angstrom. 
 You need to specify an input file with equilibrium atomic positions either by the ``--QE``, ``--VASP``, ``--xTAPP``, or ``--LAMMPS``.
 
@@ -109,7 +103,6 @@ as follows::
 
 .. important::
    In QE, you need to set tprnfor=.true. to print out atomic forces. 
-   In LAMMPS, you need to save atomic forces by adding the dump option of LAMMPS.
 
 The next step is to collect the displacement data and force data by the Python script :red:`extract.py` (also in the tools/ directory). This script can extract atomic displacements, atomic forces, and total energies from multiple output files as follows:
 
@@ -131,12 +124,6 @@ The next step is to collect the displacement data and force data by the Python s
     $ python extract.py --xTAPP=si222.cg --get=disp *.str > disp.dat
     $ python extract.py --xTAPP=si222.cg --get=force *.str > force.dat
 
-    **LAMMPS**
-    ::
-
-    $ python extract.py --LAMMPS=si222.lammps --get=disp disp*.lammps > disp.dat
-    $ python extract.py --LAMMPS=si222.lammps --get=force FORCE.* > force.dat
-
 In the above examples, atomic displacements of all the configurations are merged as *disp.dat*, and the corresponding atomic forces are saved in the file *force.dat*. These files will be used in the following fitting procedure as ``DFILE`` and ``FFILE``. (See :ref:`Format of DFILE and FFILE<label_format_DFILE>`).
 
 
@@ -230,8 +217,8 @@ For visualizing phonon dispersion relations, we provide a Python script :red:`pl
 
 Then, the phonon dispersion is shown by a pop-up window as follows:
 
-.. image:: ../img/si_phband.png
-   :scale: 60
+.. image:: ../img/Si_phband_DFT.png
+   :scale: 40
    :align: center
 
 You can save the figure as png, eps, or other formats from this window.
@@ -263,8 +250,8 @@ The command
 
 will show the phonon DOS of Si by a pop-up window:
 
-.. image:: ../img/si_phdos.png
-   :scale: 60
+.. image:: ../img/Si_phdos_DFT.png
+   :scale: 40
    :align: center
 
 To improve the resolution of DOS, try again with a denser :math:`k` grid and a smaller ``DELTA_E`` value.

diff --git a/tools/plotband.py b/tools/plotband.py
@@ -34,6 +34,7 @@
 
 # font styles
 mpl.rc('font', **{'family': 'Times New Roman', 'sans-serif': ['Helvetica']})
+mpl.rc('text', usetex=True)
 
 # line colors and styles
 color = ['b', 'g', 'r', 'm', 'k', 'c', 'y', 'r']
@@ -207,7 +208,7 @@ def get_xy_minmax(array):
     ax.xaxis.grid(True, linestyle='-')
 
     if options.print_key:
-        plt.legend(loc='lower right', prop={'size': 10})
+        plt.legend(loc='best', prop={'size': 10})
 
 #	plt.savefig('band_tmp.png', dpi=300, transparent=True)
     plt.show()
diff --git a/tools/plotdos.py b/tools/plotdos.py
@@ -185,11 +185,11 @@ def sum_atom_projected_dos(pdos_tmp, natoms_tmp):
                     counter_line += 1
 
     if options.unitname.lower() == "mev":
-        plt.xlabel("Frequency (meV)", fontsize=16, labelpad=20)
+        plt.xlabel("Frequency (meV)", fontsize=16)
     elif options.unitname.lower() == "thz":
-        plt.xlabel("Frequency (THz)", fontsize=16, labelpad=20)
+        plt.xlabel("Frequency (THz)", fontsize=16)
     else:
-        plt.xlabel("Frequency (cm${}^{-1}$)", fontsize=16, labelpad=10)
+        plt.xlabel("Frequency (cm${}^{-1}$)", fontsize=16)
 
     plt.ylabel("Phonon DOS", fontsize=16, labelpad=20)
 
@@ -214,5 +214,6 @@ def sum_atom_projected_dos(pdos_tmp, natoms_tmp):
 
     if options.print_key:
         plt.legend(loc='upper right', prop={'size': 12})
-
+
+    plt.tight_layout()
     plt.show()