Documentation update

doc/auxiliary-tools.rst

@@ -74,10 +74,19 @@ correspond to 300 K,
 
 The plot like below is displayed.
 
-.. |i0| image:: Si-kaccum.png
+.. |Si-kaccum| image:: Si-kaccum.png
         :width: 50%
 
-|i0|
+|Si-kaccum|
+
+With :math:`19\times 19\times 19` mesh:
+
+.. |Si-kaccum-m191919| image:: Si-kaccum-m191919.png
+        :width: 25%
+
+|Si-kaccum-m191919|
+
+
 
 General options
 ~~~~~~~~~~~~~~~~
@@ -99,7 +108,7 @@ POSCAR-unitcell``.
 Let ``phono3py-kaccum`` read a Pwscf unit cell file with ``-c``
 option, for example::
 
-   phono3py-kaccum --pwscf --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c Si.in --temperature=300 kappa-m191919.hdf5
+   phono3py-kaccum --pwscf --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" -c Si.in kappa-m191919.hdf5
 
 .. |ipwscf| image:: Si-kaccum-pwscf.png
                     :width: 25%

doc/command-options.rst

@@ -902,7 +902,7 @@ values given as follows, respectively,
 
 ::
 
-   % phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" --nac --jdos --ga="0 0 0  8 8 8"
+   % phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8"
 
 When temperatures are specified, two classes of weighted JDOS are
 calculated. The result is written into
@@ -926,7 +926,16 @@ the values given as follows, respectively,
 
 ::
 
-   % phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" --nac --jdos --ga="0 0 0  8 8 8" --ts=300
+   % phono3py --fc2 --dim="2 2 2" -c POSCAR-unitcell --mesh="16 16 16" --jdos --ga="0 0 0  8 8 8" --ts=300
+
+This is an example of ``Si-PBEsol``.
+
+.. |Si-JDOS| image:: Si-JDOS.png
+                     :width: 50%
+
+|Si-JDOS|
+
+
 
 ``--num-freq-points``, ``--freq-pitch``: Sampling frequency for distribution functions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1019,8 +1028,18 @@ Band path mode::
 
    % phono3py --fc3 --fc2 --dim="2 2 2" -v -c POSCAR-unitcell --nac --gruneisen --band="0 0 0  0 0 1/2"
 
-Input and output file names
-----------------------------
+File I/O
+--------
+
+``--hdf5-compression``: Choice of HDF5 compression filter
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Most of phono3py HDF5 output file is compressed by default with the
+``gzip`` compression filter. To avoid compression,
+``--hdf5-compression=None`` has to be set. Other filters (``lzf`` or
+integer values of 0 to 9) may be used, see h5py
+documentation
+(http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline).
 
 .. _output_filename_option:
 

doc/conf.py

@@ -12,7 +12,6 @@
 # serve to show the default.
 
 import sys, os
-import sphinx_bootstrap_theme
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -94,7 +93,64 @@ pygments_style = 'sphinx'
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 # html_theme = 'default'
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+################
+# guzzle theme #
+################
+# import guzzle_sphinx_theme
+
+# html_theme_path = guzzle_sphinx_theme.html_theme_path()
+# html_theme = 'guzzle_sphinx_theme'
+
+# # Register the theme as an extension to generate a sitemap.xml
+# extensions.append("guzzle_sphinx_theme")
+
+# # Guzzle theme options (see theme.conf for more information)
+# html_theme_options = {
+
+#     # Set the path to a special layout to include for the homepage
+#     "index_template": "special_index.html",
+
+#     # Set the name of the project to appear in the left sidebar.
+#     "project_nav_name": "Project Name",
+
+#     # Set your Disqus short name to enable comments
+#     "disqus_comments_shortname": "my_disqus_comments_short_name",
+
+#     # Set you GA account ID to enable tracking
+#     "google_analytics_account": "my_ga_account",
+
+#     # Path to a touch icon
+#     "touch_icon": "",
+
+#     # Specify a base_url used to generate sitemap.xml links. If not
+#     # specified, then no sitemap will be built.
+#     "base_url": "",
+
+#     # Allow a separate homepage from the master_doc
+#     "homepage": "index",
+
+#     # Allow the project link to be overriden to a custom URL.
+#     "projectlink": "http://myproject.url",
+
+#     # Visible levels of the global TOC; -1 means unlimited
+#     # "globaltoc_depth": 3,
+
+#     # If False, expand all TOC entries
+#     # "globaltoc_collapse": False,
+
+#     # If True, show hidden TOC entries
+#     # "globaltoc_includehidden": False,
+# }
+
+###################
+# bootstrap theme #
+###################
+import sphinx_bootstrap_theme
 html_theme = 'bootstrap'
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -169,11 +225,6 @@ html_theme_options = {
     'nosidebar': "true",
 }
 
-
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 #html_title = None