Merge branch 'rc'

.travis.yml

@@ -4,7 +4,7 @@ dist: trusty
 
 python:
     - '2.7'
-    - '3.5'
+    # - '3.5'
     - '3.6'
 
 before_install:

doc/changelog.rst

@@ -3,6 +3,11 @@
 Change Log
 ==========
 
+xxx-xx-2018
+-----------
+
+* ``FULL_FORCE_CONSTANTS`` tag is created (:ref:`full_force_constants_tag`).
+
 Apr-21-2018: Version 1.13.0
 ----------------------------
 

doc/command-options.rst

@@ -32,6 +32,7 @@ tags:
 * ``--fmax`` (``FMAX``)
 * ``--fmin`` (``FMIN``)
 * ``--fpitch`` (``FPITCH``)
+* ``--full-fc`` (``FULL_FORCE_CONSTANTS``)
 * ``--gc``, ``--gamma_center`` (``GAMMA_CENTER``)
 * ``--gv``, ``--group_velocity`` (``GROUP_VELOCITY = .TRUE.``)
 * ``--gv-delta-q`` (``GV_DELTA_Q``)

doc/conf.py

@@ -169,6 +169,8 @@ html_theme_options = {
     # Choose Bootstrap version.
     # Values: "3" (default) or "2" (in quotes)
     'bootstrap_version': "3",
+
+    'nosidebar': "true",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.

doc/input-files.rst

@@ -141,7 +141,7 @@ these files are controlled by :ref:`force constants tags
 use ``q2r.x`` to create force constants file by followng the
 instraction shown at :ref:`qe_q2r`
 
-Force constants are stored in an array whose shape is either
+Force constants are stored in an array of the shape either
 
 (1) ``(n_satom, n_satom, 3, 3)``
 (2) ``(n_patom, n_satom, 3, 3)``

doc/output-files.rst

@@ -146,7 +146,7 @@ the supercell axes.
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Phonopy configurations and crystal structures are stored to remember
-what a user executed. 
+what a user executed.
 
 ``.hdf5`` files
 ^^^^^^^^^^^^^^^^^
@@ -189,9 +189,9 @@ eigenvector    Eigenvector at each phonon mode.
                the primitive cell. The real and imaginary values
                correspond to the left and right, respectively.
                A set of eigenvectors comprising all bands at a q-point
-               forms a unitary matrix obtained as the result of 
+               forms a unitary matrix obtained as the result of
                numpy.linalg.eigh, i.e., LAPACK of routine _heevd.
-               Therefore eigenvectors correspond to the column vectors 
+               Therefore eigenvectors correspond to the column vectors
                of the unitary matrix.
 group_velocity Group velocity at each phonon mode in the
                Cartesian coordinates defined in the unit cell.
@@ -206,8 +206,8 @@ mesh           Numbers of mesh sampling points along axes of the
                primitive cell.
 weight         In the mesh sampling mode, only phonons at irreducible
                q-points are calculated in the default behavior. This
-	       value means the multiplicity of a q-point in the
-	       reciprocal space of the primitive cell.
+               value means the multiplicity of a q-point in the
+               reciprocal space of the primitive cell.
 ============== =======================================================
 
 Band structure mode
@@ -217,8 +217,8 @@ Band structure mode
 ============== =======================================================
 distance       In the band structure mode, this value means the
                distance from the origin in the reciprocal space of the
-	       primitive cell. The unit is the reciprocal of length
-	       unit used in the real space.
+               primitive cell. The unit is the reciprocal of length
+               unit used in the real space.
 ============== =======================================================
 
 
@@ -238,4 +238,3 @@ when phonopy ran with proper physical units. See
 direction      A displacement in the reduced coordinates.
 displacement   A displacement in the Cartesian coordinates.
 ============== =======================================================
-

doc/setting-tags.rst

@@ -1009,43 +1009,6 @@ Mind that the other symmetries of force constants, i.e., the
 symmetry from crystal symmetry or rotational symmetry, are broken to
 use ``FC_SYMMETRY``.
 
-.. Tolerance of the crystal symmetry search is given by phonopy option of
-.. ``--tolerance``.
-
-.. ``TRANSLATION``
-.. ~~~~~~~~~~~~~~~
-
-.. Translational invariance is forced by setting ``TRANSLATION =
-.. .TRUE.``. The default value is ``.FALSE.``. The input forces are
-.. summed up in each Cartesian axis and the average are subtracted from
-.. the forces.
-
-.. ``PERMUTATION``
-.. ~~~~~~~~~~~~~~~
-
-.. Symmetry of force constants:
-
-.. .. math::
-
-..    \Phi_{ij}^{\alpha\beta}
-..         = \frac{\partial^2 U}{\partial u_i^\alpha \partial u_j^\beta}
-..         = \frac{\partial^2 U}{\partial u_j^\beta \partial u_i^\alpha}
-..      = \Phi_{ji}^{\beta\alpha}
-
-.. is imposed with ``PERMUTATION = .TRUE.``. The default value is
-.. ``.FALSE.``. This is not necessary to be set, because dynamical
-.. matrix is always forced to be Hermitian in phonopy, i.e.,
-.. :math:`D^{\alpha\beta}_{ij} = (D^{\beta\alpha}_{ji})^*`.
-
-.. ``MP_REDUCE``
-.. ~~~~~~~~~~~~~~
-
-.. When mesh sampling, time reversal symmetry is imposed by setting
-.. ``MP_REDUCE = .TRUE.``. The default value is ``.TRUE.``. If you don't
-.. want time reversal symmetry, you have to set as ``MP_REDUCE =
-.. .FALSE.``.
-
-
 .. _force_constants_tag:
 
 Force constants
@@ -1067,6 +1030,17 @@ READ``, force constants are read from ``FORCE_CONSTANTS`` file. With
 The file format of ``FORCE_CONSTANTS`` is shown
 :ref:`here <file_force_constants>`.
 
+.. _full_force_constants_tag:
+
+``FULL_FORCE_CONSTANTS``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+``FULL_FORCE_CONSTANTS = .TRUE.`` is used to compute full supercell
+constants matrix. The default setting is ``.FALSE.``. By ``.TRUE.`` or
+``.FALSE.``, the array shape becomes ``(n_patom, n_satom, 3, 3)`` or
+``(n_satom, n_satom, 3, 3)``, respectively. The detail is found at
+:ref:`file_force_constants`.
+
 ``READ_FORCE_CONSTANTS``
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 

phonopy/cui/settings.py

@@ -1356,7 +1356,7 @@ class PhonopyConfParser(ConfParser):
 
         if 'is_full_fc' in arg_list:
             if self._args.is_full_fc:
-                self._confs['full_fc'] = '.true.'
+                self._confs['full_force_constants'] = '.true.'
 
         if 'fits_debye_model' in arg_list:
             if self._args.fits_debye_model:
@@ -1521,8 +1521,8 @@ class PhonopyConfParser(ConfParser):
                 if confs['write_force_constants'].lower() == '.true.':
                     self.set_parameter('write_force_constants', True)
 
-            if conf_key == 'full_fc':
-                if confs['full_fc'].lower() == '.true.':
+            if conf_key == 'full_force_constants':
+                if confs['full_force_constants'].lower() == '.true.':
                     self.set_parameter('is_full_fc', True)
 
             if conf_key == 'cutoff_radius':