Write document and update script slightly for --write-phonon and --read-phonon

doc/changelog.rst

@@ -3,6 +3,12 @@
 Change Log
 ==========
 
+Nov-29-2017
+-------------------
+
+- Documentation of ``--write-phonon`` and ``--read-phonon`` options is
+  written.
+
 Nov-22-2017: version 1.12.5
 -----------------------------
 

doc/command-options.rst

@@ -720,6 +720,36 @@ be equivalent between them.
    format. This file can be huge and usually it is not recommended to
    write it out.
 
+.. _write_phonon_option:
+
+``--write-phonon``
+~~~~~~~~~~~~~~~~~~~
+
+Phonon frequencies, eigenvectors, and grid point addresses are stored
+in ``phonon-mxxx.hdf5`` file. After writing phonons, phono3py stops
+without going to calculation.
+
+::
+
+   % phono3py --fc2 --dim="2 2  2" --mesh="16 16 16" -c POSCAR-unitcell \
+     --nac --write-phoonon
+
+.. _read_phonon_option:
+
+``--read-phonon``
+~~~~~~~~~~~~~~~~~~
+
+Phonon frequencies, eigenvectors, and grid point addresses are read
+from ``phonon-mxxx.hdf5`` file and the calculation is continued using
+these phonon values. This is useful when we want to use fixed phonon
+eigenvectors that can be different for degenerate bands when using
+different eigenvalue solvers or different CPU architectures.
+
+::
+
+   % phono3py --fc2 --fc3 --dim="2 2  2" --mesh="16 16 16" -c POSCAR-unitcell \
+     --nac --read-phoonon --br
+
 .. _ise_option:
 
 ``--ise``: Imaginary part of self energy

phono3py/file_IO.py

@@ -1067,6 +1067,8 @@ def write_gamma_detail_to_hdf5(temperature,
             w.create_dataset('frequency_point', data=frequency_points)
         return full_filename
 
+    return None
+
 def write_phonon_to_hdf5(frequency,
                          eigenvector,
                          grid_address,
@@ -1082,30 +1084,34 @@ def write_phonon_to_hdf5(frequency,
         w.create_dataset('eigenvector', data=eigenvector)
         return full_filename
 
+    return None
+
 def read_phonon_from_hdf5(mesh,
                           filename=None,
                           verbose=True):
     suffix = _get_filename_suffix(mesh, filename=filename)
-    hdf5_filename = "phonon" + suffix + ".hdf5"
-    if not os.path.exists(hdf5_filename):
+    full_filename = "phonon" + suffix + ".hdf5"
+    if not os.path.exists(full_filename):
         if verbose:
-            print("%s not found." % hdf5_filename)
-        return (None, None, None, None, hdf5_filename)
+            print("%s not found." % full_filename)
+        return (None, None, None, None, full_filename)
 
-    with h5py.File(hdf5_filename, 'r') as f:
+    with h5py.File(full_filename, 'r') as f:
         frequencies = np.array(f['frequency'][:], dtype='double', order='C')
         itemsize = frequencies.itemsize
         eigenvectors = np.array(f['eigenvector'][:],
                                 dtype=("c%d" % (itemsize * 2)), order='C')
         mesh_in_file = np.array(f['mesh'][:], dtype='intc')
         grid_address = np.array(f['grid_address'][:], dtype='intc', order='C')
-        return (frequencies,
-                eigenvectors,
-                mesh_in_file,
-                grid_address,
-                hdf5_filename)
 
-    return (None, None, None, None, hdf5_filename)
+        assert (mesh_in_file == mesh).all(), "Mesh numbers are inconsistent."
+
+        if verbose:
+            print("Phonons are read from \"%s\"." % full_filename)
+
+        return frequencies, eigenvectors, grid_address
+
+    return None
 
 def write_ir_grid_points(mesh,
                          mesh_divs,

scripts/phono3py

@@ -648,8 +648,7 @@ if run_mode is not None:
         filename = phono3py.write_phonons(filename=output_filename)
         if filename:
             if log_level:
-                print("All phonons on grid points are written into \"%s\"." %
-                      filename)
+                print("Phonons are written into \"%s\"." % filename)
                 print_end()
             sys.exit(0)
         else:
@@ -660,21 +659,19 @@ if run_mode is not None:
     if settings.get_read_phonon():
         phonons = read_phonon_from_hdf5(mesh,
                                         filename=input_filename,
-                                        verbose=log_level)
-        if phonons[0] is None:
-            print("Reading phonons from \"%s\" failed." % phonons[4])
+                                        verbose=(log_level > 0))
+        if phonons is None:
+            print("Reading phonons failed.")
             if log_level:
                 print_error()
             sys.exit(1)
+
         frequencies = phonons[0]
         eigenvectors = phonons[1]
-        grid_address = phonons[3]
+        grid_address = phonons[2]
         if phono3py.set_phonon_data(frequencies, eigenvectors, grid_address):
-            if log_level:
-                print("Phonons are read from \"%s\"." % phonons[4])
+            pass
         else:
-            print("Phonon data in %s are inconsistent to the calculation "
-                  "setting." % phonons[4])
             if log_level:
                 print_error()
             sys.exit(1)