From 95d7263503087d9c6b5e4017520aff3f9f2bc2d6 Mon Sep 17 00:00:00 2001 From: Atsushi Togo Date: Fri, 20 Oct 2017 12:42:14 +0900 Subject: [PATCH] Update document for v1.12.0 --- doc/conf.py | 6 +++--- doc/interfaces.rst | 23 +++++++++++++---------- doc/procedure.rst | 40 ++-------------------------------------- 3 files changed, 18 insertions(+), 51 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 179fc0d8..a1416545 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -49,9 +49,9 @@ copyright = u'2009, Atsushi Togo' # built documents. # # The short X.Y version. -version = '1.11.14' +version = '1.12.0' # The full version, including alpha/beta/rc tags. -release = '1.11.14' +release = '1.12.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. @@ -246,7 +246,7 @@ htmlhelp_basename = 'phonopydoc' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('contents', 'phonopy.tex', u'phonopy manual', + ('documentation', 'phonopy.tex', u'phonopy manual', u'Atsushi Togo', 'manual'), ] diff --git a/doc/interfaces.rst b/doc/interfaces.rst index d354491f..4726b2fc 100644 --- a/doc/interfaces.rst +++ b/doc/interfaces.rst @@ -75,15 +75,18 @@ Default unit conversion factor for non-analytical term correction CRYSTAL | 14.399652 -.. _interfaces_to_force_calculators: +.. _tutorials_for_calculators: -Interfaces to force calculators --------------------------------- +Tutorials for calculators +-------------------------- + +Force calculators +^^^^^^^^^^^^^^^^^^^ Short tutorials for force calculators are found in the following pages. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 vasp wien2k @@ -93,26 +96,26 @@ Short tutorials for force calculators are found in the following pages. elk crystal -Interface to VASP DFPT force constants ---------------------------------------- +VASP DFPT force constants +^^^^^^^^^^^^^^^^^^^^^^^^^^^ Using VASP DFPT feature, force constants are directly calculated. Phonopy VASP DFPT interface reads ``vasprun.xml`` and creates ``FORCE_CONSTANTS`` file. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 vasp-dfpt -Interface to FHI-aims forces ------------------------------ +For FHI-aims +^^^^^^^^^^^^^ For FHI-aims, there is a special command, ``phonopy-FHI-aims``. This tool is maintained by FHI-aims community and questions may be sent to the FHI-aims mailing list. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 FHI-aims diff --git a/doc/procedure.rst b/doc/procedure.rst index 4bf10a56..2a533cb6 100644 --- a/doc/procedure.rst +++ b/doc/procedure.rst @@ -4,41 +4,5 @@ Short tutorials ================ Tutorials for different force calculators, VASP, WIEN2k, PWscf (QE), -ABINIT, SIESTA, Elk, and, CRYSTAL, are given at -:ref:`interfaces_to_force_calculators`. - -The structure file names are different in different force calculators, -see :ref:`calculator_interfaces`. To notify this, (*) is put -after the structure file name. By refering -:ref:`calculator_interfaces`, please read the file name according to -those for the other calculators. - -Following files are required in your working directory. - -- ``POSCAR`` (*), and ``FORCE_SETS`` or ``FORCE_CONSTANTS`` -- ``disp.yaml`` is required to create ``FORCE_SETS``. - -In the case of finite difference approach, there are three steps. - -1. Create supercells and introduce atomic displacements. Each - supercell contains one atomic displacement. It is done by using - ``-d`` option with ``--dim`` option that specifies supercell - dimension. The files of supercells with atomic displacements like - as ``POSCAR-001``, ``POSCAR-002``, ..., (*) are created in current - directory by running phonopy. The files ``disp.yaml`` and - ``SPOSCAR`` are also created. The file ``SPOSCAR`` is the perfect - supercell that contains no atomic displacement. This file is not - usually used. - -2. Calculate forces on atoms of the supercells with atomic - displacements. After obtaining forces on atoms that calculated by - some calculator (it's out of phonopy), the forces are summarized in - ``FORCE_SETS`` file following the :ref:`format `. - -3. Calculate phonon related properties. - -If you already have force constants, the first and second steps can be -omitted. However your force constants have to be converted to the -:ref:`format ` that phonopy can read. The -:ref:`VASP interface ` to convert force -constants is prepared in phonopy. +ABINIT, SIESTA, Elk, and, CRYSTAL, are found at +:ref:`tutorials_for_calculators`.