Merge rc

doc/command-options.rst

@@ -412,6 +412,8 @@ No log is shown.
 Crystal symmetry
 -----------------
 
+.. _tolerance_option:
+
 ``--tolerance``
 ~~~~~~~~~~~~~~~
 
@@ -422,6 +424,8 @@ crystal structure. The default value is 1e-5.
 
    % phonopy --tolerance=1e-3
 
+.. _symmetry_option:
+
 ``--symmetry``
 ~~~~~~~~~~~~~~
 

doc/documentation.rst

@@ -6,6 +6,7 @@ Documentation
    :maxdepth: 1
 
    install
+   symmetry
    Tutorial <procedure>
    workflow
    examples

doc/index.rst

@@ -69,6 +69,7 @@ Documentation
    :maxdepth: 1
 
    install
+   symmetry
    Tutorial <procedure>
    workflow
    examples

doc/symmetry.rst

@@ -0,0 +1,46 @@
+Crystal symmetry
+=================
+
+Tolerance used in crystal symmetry search
+------------------------------------------
+
+Phonon calculation is based on the assumption that atoms have thier
+own equilibrium positions where forces on these atoms are zero. In
+addition, there is a unit cell that contains these atoms and the unit
+cell are repeated in the direct space, i.e., it forms a lattice. The
+lattice vectors (or basis vectors) and points of atoms in this unit
+cell give the information of the crystal structure.
+
+The crystal structure may have a specific symmetry. The categorization
+of the crystal symmetried is achieved by the group theory about
+symmetry operations, and there are the 230 different space group
+types. In phonopy, the crystal symmetry is automatically analyzed from
+the input unit cell structure file that doesn't contain the symmetry
+information. Symmetries are searched by attemping possible symmetry
+operations to the crsytal structure and cheking if the crystal
+structure after the symmetry operation is overlapping to the original
+crystal structures. In this analysis, a tolerance of distance is
+used to tolerate small deviation of overlapping. This tolerance is
+the user's choice. The default value is ``1e-5``.
+
+Often we know the space group type of our crystal. Therefore it is
+recommended to check whether the space group type of the input unit
+cell is the correct one or not with very tight value such as
+``--tolerance=1e-8`` using :ref:`tolerance_option` option. If an input
+unit cell structure is naively distorted for which the distortion is
+about the same order of the chosen tolerance, inconsistency in
+symmetry handling may occur and it can result in a crash of the
+calculation or induce a strange calculation result. This can be
+checked by changing the tolerance value variously and watching the
+obtained space group type. If an input unit cell structure is
+distorted, different space group types are found with respect to the
+different tolerance values.
+
+The detailed space group information is obtained by
+:ref:`symmetry_option` option. As a result of using this option and
+the chosen tolerance value, ``BPOSCAR`` file is obtained. This is a
+standardized conventional unit cell (see
+https://atztogo.github.io/spglib/definition.html#conventions-of-standardized-unit-cell),
+and its distortion against the crystal symmetry is very small. It is
+recommended to used this structure as the starting point of phonopy
+calculation.

phonopy/interface/FHIaims.py

@@ -131,7 +131,7 @@ def read_aims_output(filename):
     N = 0
     while l < len(lines):
         line = lines[l]
-        if "Number of atoms" in line:
+        if "| Number of atoms" in line:
             N = int(line.split()[5])
         elif "| Unit cell:" in line:
             cell = []

phonopy/phonon/irreps.py

@@ -559,7 +559,52 @@ character_table = {
     '-6': None,
 
     # C6h (23)
-    '6/m': None,
+    '6/m': 
+    [{'rotation_list': ('E', 'C6', 'C3', 'C2', 'i', 'S3', 'S6', 'sgh'),
+      'character_table': {'Ag':  ( 1, 1, 1, 1, 1, 1, 1, 1 ),
+                          'Bg':  ( 1,-1, 1,-1, 1,-1, 1,-1 ),
+                          'E1g': ( 2, 1,-1,-2, 2, 1,-1,-2 ),
+                          'E2g': ( 2,-1,-1, 2, 2,-1,-1, 2 ),
+                          'Au':  ( 1, 1, 1, 1,-1,-1,-1,-1 ),
+                          'Bu':  ( 1,-1, 1,-1,-1, 1,-1, 1 ),
+                          'E1u': ( 2, 1,-1,-2,-2,-1, 1, 2 ),
+                          'E2u': ( 2,-1,-1, 2,-2, 1, 1,-2 )},
+      'mapping_table': {'E'     : ((( 1, 0, 0 ),
+                                    ( 0, 1, 0 ),
+                                    ( 0, 0, 1 )),),
+                        'C6'    : ((( 1,-1, 0 ),
+                                    ( 1, 0, 0 ),
+                                    ( 0, 0, 1 )),
+                                   (( 0, 1, 0 ),
+                                    (-1, 1, 0 ),
+                                    ( 0, 0, 1 )),),
+                        'C3'    : ((( 0,-1, 0 ),
+                                    ( 1,-1, 0 ),
+                                    ( 0, 0, 1 )),
+                                   ((-1, 1, 0 ),
+                                    (-1, 0, 0 ),
+                                    ( 0, 0, 1 )),),
+                        'C2'    : (((-1, 0, 0 ),
+                                    ( 0,-1, 0 ),
+                                    ( 0, 0, 1 )),),
+                        'i'     : (((-1, 0, 0 ),
+                                    ( 0,-1, 0 ),
+                                    ( 0, 0,-1 )),),
+                        'S3'    : (((-1, 1, 0 ),
+                                    (-1, 0, 0 ),
+                                    ( 0, 0,-1 )),
+                                   (( 0,-1, 0 ),
+                                    ( 1,-1, 0 ),
+                                    ( 0, 0,-1 )),),
+                        'S6'    : ((( 0, 1, 0 ),
+                                    (-1, 1, 0 ),
+                                    ( 0, 0,-1 )),
+                                   (( 1,-1, 0 ),
+                                    ( 1, 0, 0 ),
+                                    ( 0, 0,-1 )),),
+                        'sgh'   : ((( 1, 0, 0 ),
+                                    ( 0, 1, 0 ),
+                                    ( 0, 0,-1 )),)}}],
 
     # D6 (24)
     '622': None,