Set version v1.17.0 and update documentation for v1.17.0

doc/changelog.rst

@@ -3,6 +3,21 @@
 Change Log
 ==========
 
+Apr-18-2019: Version 1.17.0
+---------------------------
+- ``--cfz`` option was made to subtract residual forces. See
+  :ref:`cfz_option`.
+- ``--cutoff-pair`` was made to override the cutoff pair distance
+  written in ``disp_fc3.yaml`` when using on calculating force
+  constants. This is useful when checking cutoff distance
+  dependency. So the use case of having fully computed ``FORCES_FC3``
+  is assumed.
+- TURBOMOLE interface is provided by Antti Karttunen
+  (``--turbomole``).
+- Compatibility of ``fc2.hdf5`` and ``force_constants.hdf5`` was
+  improved for all calculators to store physical unit information in
+  the hdf5 file. See :ref:`file_format_compatibility`.
+
 Mar-24-2019: Version 1.16.0
 ---------------------------
 - Bug fixes and catching up the updates of phonopy.

doc/command-options.rst

@@ -273,6 +273,24 @@ necessary to run with ``--dim_fc2`` option.
 
    % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
 
+.. _cfz_option:
+
+``--cfz``: Create ``FORCES_FC3`` and ``FORCES_FC2`` subtracting residual forces
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is used to create ``FORCES_FC3`` and ``FORCES_FC2`` subtracting
+residual forces combined with ``--cf3`` and ``--cf2``,
+respectively. In the following example, it is supposed that
+``disp3-00000/vasprun.xml`` and ``disp2-00000/vasprun.xml`` contain
+the forces of the perfect supercells. In ideal case, these forces are
+zero, but often they are not. Here, this is called "residual
+forces". Sometimes quality of force constants is improved in this way.
+
+::
+
+   % phono3py --cf3 disp3-{00001..01254}/vasprun.xml --cfz disp3-00000/vasprun.xml
+   % phono3py --cf2 disp2-{00001..00006}/vasprun.xml --cfz disp2-00000/vasprun.xml
+
 .. _fs2f2_option:
 
 ``--fs2f2`` or ``--force-sets-to-forces-fc2``

doc/conf.py

@@ -49,9 +49,9 @@ copyright = u'2015, Atsushi Togo'
 # built documents.
 #
 # The short X.Y version.
-version = '1.16.0'
+version = '1.17'
 # The full version, including alpha/beta/rc tags.
-release = '1.16.0'
+release = '1.17.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/tips.rst

@@ -113,7 +113,7 @@ File format compatibility with phonopy
 ---------------------------------------
 
 - ``disp_fc3.yaml`` and ``disp_fc2.yaml`` are not compatible with
-  phonopy's ``disp.yaml``.
+  phonopy's ``phonopy_disp.yaml``.
 - ``FORCES_FC3`` and ``FORCES_FC2`` are not
   compatible with phonopy's ``FORCE_SETS``.
 - ``FORCE_SETS`` can be created using :ref:`--cfs <cfs_option>` from

doc/turbomole.rst

@@ -1,9 +1,9 @@
 .. _turbomole_interface:
 
 TURBOMOLE & phono3py calculation
-==============================
+================================
 
-The riper module of TURBOMOLE can be used to study periodic structures. 
+The riper module of TURBOMOLE can be used to study periodic structures.
 An example for TURBOMOLE is found in the ``example/Si-TURBOMOLE`` directory.
 
 To invoke the TURBOMOLE interface, ``--turbomole`` option has to be always
@@ -14,7 +14,7 @@ specified::
 When the file name of the unit cell is different from the default one
 (see :ref:`default_unit_cell_file_name_for_calculator`), ``-c`` option
 is used to specify the file name. TURBOMOLE unit cell file parser used in
-phono3py is the same as that in phonopy. It reads a limited number of 
+phono3py is the same as that in phonopy. It reads a limited number of
 keywords that are documented in the phonopy web site
 (http://atztogo.github.io/phonopy/turbomole.html#turbomole-interface).
 
@@ -27,7 +27,7 @@ In the example Si-TURBOMOLE, the TURBOMOLE input file is ``control``.
 This is the default file name for the TURBOMOLE interface,
 so the ``-c control`` parameter is not needed.
 
-1) Create supercells with displacements (2x2x2 conventional cell for 
+1) Create supercells with displacements (2x2x2 conventional cell for
    3rd order FC and 3x3x3 conventional cell for 2nd order FC)
 
    ::
@@ -46,8 +46,8 @@ so the ``-c control`` parameter is not needed.
    displacement are what we need for the phonon calculation. To get accurate
    forces, $scfconv should be 10. Phono3py includes this data group automatically
    in the ``control`` file. You also need to choose a k-point mesh for the force
-   calculations. TURBOMOLE data group $riper may need to be adjusted to improve 
-   SCF convergence (see example files in subdirectory supercell-00001 for 
+   calculations. TURBOMOLE data group $riper may need to be adjusted to improve
+   SCF convergence (see example files in subdirectory supercell-00001 for
    further details)
 
    Then, TURBOMOLE supercell calculations are executed to obtain forces on

phono3py/version.py

@@ -32,4 +32,4 @@
 # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-__version__ = "1.16.0"
+__version__ = "1.17.0"

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>=2.1.2'],
+                                'phonopy>=2.1.3'],
               provides=['phono3py'],
               scripts=scripts_phono3py,
               ext_modules=[extension_lapackepy, extension_phono3py],