Phonopy document minor update

doc/command-options.rst

@@ -1,4 +1,4 @@
-.. _command_options:
+x.. _command_options:
 
 Command options
 ===============

doc/conf.py

@@ -46,9 +46,9 @@ copyright = u'2009, Atsushi Togo'
 # built documents.
 #
 # The short X.Y version.
-version = '1.9.7'
+version = '1.10.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.9.7'
+release = '1.10.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/index.rst

@@ -27,7 +27,7 @@ release toward python 3 support.
 
 **Phono3py** for phonon-phonon interaction calculations has been 
 released as an open beta
-version. See the document at http://phonopy.sourceforge.net/phono3py/
+version. See the document at http://atztogo.github.io/phono3py/
 .
 
 **Phonon database**: A collection of phonon and mode-Gruneisen
@@ -102,13 +102,6 @@ Documentation
    reference
    changelog
 
-
-- `Manual in PDF <https://sourceforge.net/projects/phonopy/files/phonopy%20documentation/phonopy-manual.pdf/download>`_
-
-- `Presentation: Introduction to phonopy <https://sourceforge.net/projects/phonopy/files/phonopy%20documentation/phonopy-workshop.pdf/download>`_
-
-- `Presentation: Introduction to phonons <http://sourceforge.net/projects/phonopy/files/phonopy%20documentation/introduction-phonon-calc.pdf/download>`_
-
 .. _mailinglist:
 
 Mailing list

doc/install.rst

@@ -5,7 +5,7 @@ Download and install
 
 The procedure of setup phonopy is explained in this section. It is
 supposed that phonopy is installed on the recent linux distribution
-like Ubuntu or Fedora with Python version 2.5 or later. Mac OS X users
+like Ubuntu or Fedora with Python version 2.6 or later. Mac OS X users
 may find some more information on :ref:`install_MacOSX`. If you met
 installation problems, it is recommended to prepare a system with
 Ubuntu linux as a virtual machine. See :ref:`virtualmachine`
@@ -37,22 +37,27 @@ Ubuntu linux as a virtual machine. See :ref:`virtualmachine`
 
    and extract it::
 
-   % tar xvfz phonopy-1.9.7.tar.gz
+   % tar xvfz phonopy-1.10.0.tar.gz
 
-3. Put your phonopy directory into your ``PYTHONPATH`` in .bashrc etc,
-   e.g.::
-
-      export PYTHONPATH=~/phonopy-1.9.7/lib/python
-
-4. Set up C-libraries for python C-API and python codes. This can be
+3. Set up C-libraries for python C-API and python codes. This can be
    done as follows:
 
    Run ``setup.py`` script::
 
-   % python setup.py install --home=.
+      % python setup.py install --home=<my-directory>
 
-   The command ``phonopy`` is located in the ``bin`` directory. The
-   install location can be specified by the option ``--home``.
+   where :file:`{<my-directory>}` may be your current directory, :file:`.`.
+   Another choice may be to use the user scheme (see the python document)::
+
+      % python setup.py install --user
+
+   The executable command ``phonopy`` is located in the ``bin`` directory.
+
+4. Put ``lib/python`` path into :envvar:`$PYTHONPATH`, e.g., in your
+   .bashrc, .zshenv, etc. If it is installed under your current
+   directory, the path to be added to :envvar:`$PYTHONPATH` is such as below::
+
+      export PYTHONPATH=~/phonopy-1.10.0/lib/python
 
 
 Special cases on installation
@@ -63,4 +68,3 @@ Special cases on installation
 
    MacOSX   
    virtualmachine
-

doc/siesta.rst

@@ -43,7 +43,7 @@ The procedure of a Siesta-phonopy calculation is the following:
 
    ::
    
-     % phonopy --siesta -f disp-001/si.FA ...
+     % phonopy --siesta -f disp-001/Si.FA ...
 
    Here ``*.FA`` files are the forces files created by Siesta.
    To run this command, ``disp.yaml`` has to be