Update PH_Q2R class and its document

doc/conf.py

@@ -49,9 +49,9 @@ copyright = u'2009, Atsushi Togo'
 # built documents.
 #
 # The short X.Y version.
-version = '1.13.0'
+version = '1.13.2'
 # The full version, including alpha/beta/rc tags.
-release = '1.13.0'
+release = '1.13.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/input-files.rst

@@ -141,10 +141,10 @@ 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 of the shape either
+Force constants are stored in either array shape of
 
-(1) ``(n_satom, n_satom, 3, 3)``
-(2) ``(n_patom, n_satom, 3, 3)``
+- Compact format: ``(n_patom, n_satom, 3, 3)``
+- Full format: ``(n_satom, n_satom, 3, 3)``
 
 where ``n_satom`` and ``n_patom`` are the numbers of atoms in
 supercell and primitive cell, respectively.

doc/interfaces.rst

@@ -106,7 +106,7 @@ Short tutorials for force calculators are found in the following pages.
 
    vasp
    wien2k
-   pwscf
+   qe
    abinit
    siesta
    elk

doc/qe.rst

@@ -236,8 +236,6 @@ symmetrized by the translational invariance condition using
     #!/usr/bin/env python
 
     import sys
-    from phonopy.file_IO import write_FORCE_CONSTANTS
-    from phonopy.file_IO import write_force_constants_to_hdf5
     from phonopy.interface.qe import read_pwscf, PH_Q2R
 
     primcell_filename = sys.argv[1]
@@ -245,23 +243,7 @@ symmetrized by the translational invariance condition using
     cell, _ = read_pwscf(primcell_filename)
     q2r = PH_Q2R(q2r_filename)
     q2r.run(cell)
-    write_force_constants_to_hdf5(q2r.fc)
-    # write_FORCE_CONSTANTS(q2r.fc)
-
-..
-      import numpy as np
-      from phonopy.structure.symmetry import elaborate_borns_and_epsilon
-      if q2r.epsilon is not None:
-          borns, epsilon, _ = elaborate_borns_and_epsilon(
-              cell,
-              q2r.borns,
-              q2r.epsilon,
-              supercell_matrix=np.diag(q2r.dimension),
-              symmetrize_tensors=True)
-          print("default")
-          print(("%13.8f" * 9) % tuple(q2r.epsilon.ravel()))
-          for z in q2r.borns:
-              print(("%13.8f" * 9) % tuple(z.ravel()))
+    q2r.write_force_constants()
 
 Saving this script as ``make_fc_q2r.py``, this is used as, e.g.,
 
@@ -269,6 +251,12 @@ Saving this script as ``make_fc_q2r.py``, this is used as, e.g.,
 
    % python make_fc_q2r.py NaCl.in NaCl.fc
 
+This gives ``force_constants.hdf5`` file in the compact format (see
+:ref:`file_force_constants`).  From version 1.13.2, full supercell
+force constants can be written by ``q2r.run(cell, is_full_fc=True)``
+instead of ``q2r.run(cell)`` in the above
+script. ``FORCE_CONSTANTS`` file instead of ``force_constants.hdf5``
+can be obtained by ``q2r.write_force_constants(fc_format='text')``.
 
 Non-analytical term correction
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

phonopy/interface/qe.py

@@ -337,13 +337,10 @@ class PH_Q2R(object):
     ---------
     #!/usr/bin/env python
 
-    from phonopy.file_IO import write_FORCE_CONSTANTS
-    from phonopy.interface.qe import read_pwscf, PH_Q2R
-
     cell, _ = read_pwscf(primcell_filename)
     q2r = PH_Q2R(q2r_filename)
     q2r.run(cell)
-    write_FORCE_CONSTANTS(q2r.fc)
+    q2r.write_force_constants()
     ---------
 
     To save memory/storage space of force constants, the shape of
@@ -390,6 +387,10 @@ class PH_Q2R(object):
         Born effective charges
         dtype='double'
         shape=(natom_prim, 3, 3)
+    primitive : Primitive
+        Primitive cell
+    supercell : Supercell
+        Supercell
 
     """
 
@@ -398,6 +399,8 @@ class PH_Q2R(object):
         self.dimension = None
         self.epsilon = None
         self.borns = None
+        self.primitive = None
+        self.supercell = None
         self._symprec = symprec
         self._filename = filename
 
@@ -429,8 +432,18 @@ class PH_Q2R(object):
             self.epsilon = fc_dct['dielectric']
             self.borns = fc_dct['born']
             if parse_fc:
-                self.fc = self._arrange_supercell_fc(
-                    cell, fc_dct['fc'], is_full_fc=is_full_fc)
+                (self.fc,
+                 self.primitive,
+                 self.supercell) = self._arrange_supercell_fc(
+                     cell, fc_dct['fc'], is_full_fc=is_full_fc)
+
+    def write_force_constants(self, fc_format='hdf5'):
+        if self.fc is not None:
+            if fc_format == 'hdf5':
+                p2s_map = self.primitive.get_primitive_to_supercell_map()
+                write_force_constants_to_hdf5(self.fc, p2s_map=p2s_map)
+            else:
+                write_FORCE_CONSTANTS(self.fc)
 
     def _parse_q2r(self, f):
         """Parse q2r output file
@@ -528,7 +541,7 @@ class PH_Q2R(object):
             fc = np.zeros((natom, natom_s, 3, 3), dtype='double', order='C')
             fc[:, :] = q2r_fc[:, site_map]
 
-        return fc
+        return fc, pcell, scell
 
     def _get_q2r_positions(self, cell):
         dim = self.dimension