From d05a8317d8b05b6089d619d21287629f2d7aa835 Mon Sep 17 00:00:00 2001
From: Atsushi Togo <atz.togo@gmail.com>
Date: Tue, 24 Jul 2018 11:18:26 +0900
Subject: [PATCH] Update document

---
 doc/_static/procedure.dot | 23 +++++++++++++++++------
 doc/index.rst             | 11 ++++++-----
 doc/workflow.rst          | 15 ++++++++++++++-
 3 files changed, 37 insertions(+), 12 deletions(-)

diff --git a/doc/_static/procedure.dot b/doc/_static/procedure.dot
index 5c588b26..25873843 100644
--- a/doc/_static/procedure.dot
+++ b/doc/_static/procedure.dot
@@ -2,14 +2,18 @@ digraph phonopy {
   graph [bgcolor=transparent];
   "Phonopy pre-process" [shape = box, style = filled];
   "Phonopy post-process" [shape = box, style = filled];
-  "Force calc." [shape = diamond];
-  "Force-constant calc." [shape = diamond];
+  "Force calc." [shape = octagon];
+  "Force-constant calc." [shape = octagon];
   "Band structure" [shape = box];
   "Mesh sampling" [shape = box];
-  "Animation" [shape = box];
+  "Atomic modulations" [shape = box];
   "Thermal properties" [shape = box];
   "DOS" [shape = box];
   "PDOS" [shape = box];
+  "Mean square displacement" [shape = box];
+  "Arbitrary q-point" [shape = box];
+  "Irreducible reps." [shape = box];
+  "Dynamic structure factor" [shape = box];
 
   "unit cell" -> "Phonopy pre-process";
   "supercell size" -> "Phonopy pre-process";
@@ -23,14 +27,21 @@ digraph phonopy {
   
   "unit cell" -> "Phonopy post-process";
   "supercell size" -> "Phonopy post-process";
-  "force constants" -> "Phonopy post-process";
   "primitive cell size" -> "Phonopy post-process";
+  "Non-analytical term\ncorrection parameters\n(optional)" -> "Phonopy post-process";
+  "force constants" -> "Phonopy post-process";
 
   "Phonopy post-process" -> "Band structure";
   "Phonopy post-process" -> "Mesh sampling";
-  "Phonopy post-process" -> "Animation" [label = "with eigenvectors"];
+  "Phonopy post-process" -> "Arbitrary q-point";
 
   "Mesh sampling" -> "DOS";
-  "Mesh sampling" -> "PDOS" [label = "with eigenvectors"];
+  "Mesh sampling" -> "PDOS";
   "Mesh sampling" -> "Thermal properties";
+  "Mesh sampling" -> "Mean square displacement";
+
+  "Mean square displacement" -> "Dynamic structure factor";
+  "Arbitrary q-point" -> "Dynamic structure factor";
+  "Arbitrary q-point" -> "Atomic modulations";
+  "Arbitrary q-point" -> "Irreducible reps.";
 }
diff --git a/doc/index.rst b/doc/index.rst
index fb9c6865..994cd1dd 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -38,11 +38,12 @@ The following features of phonopy are highlighted:
 - :ref:`Phonon group velocity <group_velocity>`
 - :ref:`Thermal ellipsoids <thermal_displacement_matrices_tag>` / :ref:`Mean square displacements <thermal_displacements_tag>`
 - :ref:`Irreducible representations of normal modes <irreducible_representation_related_tags>`
-- :ref:`Quasi-harmonic approximation <phonopy_qha>`: Thermal expansion, heat
-  capacity at constant pressure (Cp),
-- :ref:`Mode Grüneisen parameters <phonopy_gruneisen>`
+- :ref:`Dynamic structure factor for INS and IXS <dynamic_structure_factor>`
 - :ref:`Non-analytical-term correction <nac_tag>`: LO-TO splitting
   (:ref:`Born effective charges and dielectric constant are required. <born_file>`)
+- :ref:`Mode Grüneisen parameters <phonopy_gruneisen>`
+- :ref:`Quasi-harmonic approximation <phonopy_qha>`: Thermal expansion, heat
+  capacity at constant pressure (Cp),
 - :ref:`Interfaces to calculators <calculator_interfaces>`:
   :ref:`VASP <tutorial>`,
   :ref:`VASP DFPT <vasp_dfpt_interface>`,
@@ -77,9 +78,9 @@ Documentation
    output-files
    setting-tags
    command-options
-   qha
-   Mode Grüneisen parameters <gruneisen>
    dynamic-structure-factor
+   Mode Grüneisen parameters <gruneisen>
+   qha
    interfaces
    auxiliary-tools
    external-tools
diff --git a/doc/workflow.rst b/doc/workflow.rst
index b007947a..baf4b4bc 100644
--- a/doc/workflow.rst
+++ b/doc/workflow.rst
@@ -3,11 +3,14 @@
 Work flow
 ==========
 
+Phonon calculations at constant volume
+--------------------------------------
+
 Work flow of phonopy is shown schematically. There are two ways to
 calculate, (1) atomic forces from finite displacements and (2) given
 force constants. You can choose one of them. Forces on atoms or force
 constants are calculated by your favorite calculator (shown by the
-diamonds in the work flow). The boxes are jobs being done by phonopy,
+octagons in the work flow). The boxes are jobs being done by phonopy,
 and the circles are input and intermediate output data structures.
 
 .. figure:: procedure.png
@@ -16,3 +19,13 @@ and the circles are input and intermediate output data structures.
 
    Work flow of phonon calculation
 
+Combinations of phonon calculations at different volumes
+---------------------------------------------------------
+
+Mode Grüneisen parameters can be calculated from two or three phonon
+calculation results obtained at slightly different volume points. See
+the details at :ref:`phonopy_gruneisen`.
+
+With more volume points and fitting the thermal properties, thermal
+properties at constant pressure are obtained under the (so-called)
+quasi-harmonic approximation. See more details at :ref:`phonopy_qha`.