Update document

doc/command-options.rst

@@ -232,6 +232,38 @@ necessary to run with ``--dim_fc2`` option.
 
    % phono3py --cf2 disp_fc2-{00001..00002}/vasprun.xml
 
+.. _fs2f2_option:
+
+``--fs2f2`` or ``--force_sets_to_forces_fc2``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Using this option, ``FORCES_FC2`` and ``disp_fc2.yaml`` are created
+from phonopy ``FORCE_SETS`` file.
+
+::
+
+   % phono3py --fs2f2
+
+.. _cfs_option:
+
+``--cfs`` or ``--create_force_sets``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Using this option, phonopy's ``FORCE_SETS`` is created from
+``FORCES_FC3`` and ``disp_fc3.yaml``.
+
+::
+
+   % phono3py --cfs
+
+In conjunction with :ref:`--dim_fc2 <dim_fc2_option>`, phonopy's
+``FORCE_SETS`` is created from ``FORCES_FC2`` and ``disp_fc2.yaml``
+instead of ``FORCES_FC3`` and ``disp_fc3.yaml``.
+
+::
+
+   % phono3py --cfs --dim_fc2="x x x"
+
 ``--cutoff_fc3`` or ``--cutoff_fc3_distance``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

doc/output-files.rst

@@ -14,6 +14,10 @@ from HDF5 files is also shown.
 Intermediate text files
 ------------------------
 
+The following files are not compatible with phonopy. But phonopy's
+``FORCE_SETS`` file can be created using phono3py command options from
+the following files. See the detail at :ref:`file_format_compatibility`.
+
 ``disp_fc3.yaml``
 ^^^^^^^^^^^^^^^^^^
 
@@ -25,7 +29,6 @@ This is created with ``-d`` option. See :ref:`create_displacements_option`.
 This is created with ``-d`` option with ``--dim_fc2`` option. See
 :ref:`dim_fc2_option`.
 
-
 ``FORCES_FC3``
 ^^^^^^^^^^^^^^^
 

doc/tips.rst

@@ -3,6 +3,10 @@
 Tips
 =====
 
+.. contents::
+   :depth: 2
+   :local:
+
 .. _brillouinzone_sum:
 
 Brillouin zone summation
@@ -102,3 +106,17 @@ due to the numerical noise of the force calculator. Usually increasing
 the displacement distance by the :ref:`amplitude option
 <amplitude_option>` reduces the numerical noise, but as its drawback
 higher order anharmonicity is involved (renormalized) into fc3 and fc2.
+
+.. _file_format_compatibility:
+
+File format compatibility with phonopy
+---------------------------------------
+
+``disp_fc3.yaml`` and ``disp_fc2.yaml`` are not compatible with
+phonopy's ``disp.yaml``. ``FORCES_FC3`` and ``FORCES_FC2`` are not
+compatible with phonopy's ``FORCE_SETS``. But ``FORCE_SETS`` can be
+created using :ref:`--cfs <cfs_option>`, and ``FORCES_FC2`` and
+``disp_fc2.yaml`` can be created using :ref:`--fs2f2
+<fs2f2_option>`. In addition, if ``fc2.hdf5`` is renamed to
+``force_constants.hdf5``, it is used in phonopy with ``--hdf5`` and
+``--readfc`` option.

phono3py/cui/phono3py_argparse.py

@@ -218,10 +218,6 @@ def get_parser():
     parser.add_option(
         "--fc3", dest="read_fc3", action="store_true",
         help="Read third order force constants")
-    parser.add_option(
-        "--fs2f2", "--force_sets_to_forces_fc2",
-        dest="force_sets_to_forces_fc2_mode",
-        action="store_true", help="Create FORCES_FC2 from FORCE_SETS")
     parser.add_option(
         "--freq_scale", dest="frequency_scale_factor", type="float",
         help=("Squared scale factor multiplied with fc2. Therefore frequency "
@@ -229,6 +225,13 @@ def get_parser():
     parser.add_option(
         "--freq_pitch", dest="fpitch", type="float",
         help="Pitch in frequency for spectrum")
+    parser.add_option(
+        "--fs2f2", "--force_sets_to_forces_fc2",
+        dest="force_sets_to_forces_fc2_mode",
+        action="store_true", help="Create FORCES_FC2 from FORCE_SETS")
+    parser.add_option(
+        "--fst", "--frequency_shift", dest="is_frequency_shift",
+        action="store_true", help="Calculate frequency shifts")
     parser.add_option(
         "--full_pp", dest="is_full_pp",
         action="store_true",
@@ -236,15 +239,15 @@ def get_parser():
               "This may be activated when full elements of ph-ph interaction "
               "strength are needed, i.e., to calculate average ph-ph "
               "interaction strength."))
+    parser.add_option(
+        "--ga", "--grid_addresses", dest="grid_addresses", type="string",
+        help="Fixed grid addresses where anharmonic properties are calculated")
     parser.add_option(
         "--gamma_unit_conversion", dest="gamma_unit_conversion", type="float",
         help="Conversion factor for gamma")
     parser.add_option(
         "--gp", "--grid_points", dest="grid_points", type="string",
         help="Fixed grid points where anharmonic properties are calculated")
-    parser.add_option(
-        "--ga", "--grid_addresses", dest="grid_addresses", type="string",
-        help="Fixed grid addresses where anharmonic properties are calculated")
     parser.add_option(
         "--gruneisen", dest="is_gruneisen", action="store_true",
         help="Calculate phonon Gruneisen parameter")
@@ -278,9 +281,6 @@ def get_parser():
     parser.add_option(
         "--lw", "--linewidth", dest="is_linewidth",
         action="store_true", help="Calculate linewidths")
-    parser.add_option(
-        "--fst", "--frequency_shift", dest="is_frequency_shift",
-        action="store_true", help="Calculate frequency shifts")
     parser.add_option(
         "--mass", dest="masses", action="store", type="string",
         help="Same as MASS tag")
@@ -425,13 +425,13 @@ def get_parser():
     parser.add_option(
         "--write_collision", dest="write_collision", action="store_true",
         help="Write collision matrix and Gammas to files")
+    parser.add_option(
+        "--write_gamma", dest="write_gamma", action="store_true",
+        help="Write imag-part of self energy to files")
     parser.add_option(
         "--write_gamma_detail", "--write_detailed_gamma",
         dest="write_gamma_detail",
         action="store_true", help="Write out detailed imag-part of self energy")
-    parser.add_option(
-        "--write_gamma", dest="write_gamma", action="store_true",
-        help="Write imag-part of self energy to files")
     parser.add_option(
         "--write_phonon", dest="write_phonon", action="store_true",
         help="Write all phonons on grid points to files")