Update document for v1.16.0

doc/changelog.rst

@@ -3,6 +3,30 @@
 Change Log
 ==========
 
+Mar-24-2019: Version 1.16.0
+---------------------------
+- Bug fixes and catching up the updates of phonopy.
+- Most of hdf5 output files are compressed by ``gzip`` as
+  default. This compression can be set off, see
+  :ref:`hdf5_compression_option`.
+- (Experimental) ``phono3py`` command accepts ``phono3py.yaml`` type
+  file as an input crystal structure by ``-c`` option. When ``DIM``
+  and any structure file are not given, ``phono3py_disp.yaml``
+  (primary) or ``phono3py.yaml`` (secondary) is searched in the current
+  directory. Then ``phono3py.yaml`` type file is used as the input.
+  By this, semi-automatic phono3py mode is invocked, which acts as
+
+  (1) ``supercell_matrix`` corresponding to ``DIM`` in the
+      ``phono3py.yaml`` type file is used if it exists.
+  (2) ``phonon_supercell_matrix``  corresponding to ``DIM_FC2`` in the
+      ``phono3py.yaml`` type file is used if it exists.
+  (3) ``primitive_matrix`` in the ``phono3py.yaml`` type file
+      is used if it exists. Otherwise, set ``PRIMITIVE_AXES = AUTO``
+      when ``PRIMITIVE_AXES`` is not given.
+  (4) NAC params are read (``NAC = .TRUE.``) if NAC params are
+      contained (primary) in the ``phono3py.yaml`` type file or if
+      ``BORN`` file exists in the current directory (secondary).
+
 Nov-22-2018: version 1.14.3
 ----------------------------
 - Update to work with phonopy v1.14.2.

doc/command-options.rst

@@ -20,7 +20,7 @@ configuration (e.g., saved in a file ``setting.conf``) is as follow::
 
    DIM = 2 2 2
    DIM_FC2 = 4 4 4
-   PRIMITIVE_AXIS = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
+   PRIMITIVE_AXES = 0 1/2 1/2 1/2 0 1/2 1/2 1/2 0
    MESH = 11 11 11
    BTERTA = .TRUE.
    NAC = .TRUE.
@@ -145,13 +145,13 @@ usual phono3py run without ``--dim-fc2`` option.
 
 .. _pa_option:
 
-``--pa``, ``--primitive-axis``: Transformation matrix to primitive cell
+``--pa``, ``--primitive-axes``: Transformation matrix to primitive cell
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-(Setting tag: ``PRIMITIVE_AXIS``)
+(Setting tag: ``PRIMITIVE_AXES``)
 
 Transformation matrix from a non-primitive cell to the primitive
-cell. See phonopy ``PRIMITIVE_AXIS`` tag (``--pa`` option) at
+cell. See phonopy ``PRIMITIVE_AXES`` tag (``--pa`` option) at
 http://atztogo.github.io/phonopy/setting-tags.html#primitive-axis
 
 ``--fc2``: Read 2nd order force constants
@@ -1031,6 +1031,8 @@ Band path mode::
 File I/O
 --------
 
+.. _hdf5_compression_option:
+
 ``--hdf5-compression``: Choice of HDF5 compression filter
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

setup.py

@@ -286,7 +286,7 @@ if __name__ == '__main__':
               url='http://atztogo.github.io/phono3py/',
               packages=packages_phono3py,
               install_requires=['numpy', 'PyYAML', 'matplotlib', 'h5py',
-                                'phonopy>=2.1.1'],
+                                'phonopy>=2.1.2'],
               provides=['phono3py'],
               scripts=scripts_phono3py,
               ext_modules=[extension_lapackepy, extension_phono3py],