Update document

doc/auxiliary-tools.rst

@@ -190,7 +190,8 @@ convergence.
 ^^^^^^^^^
 
 Outer product of group velocities :math:`\mathbf{v}_\lambda \otimes
-\mathbf{v}_\lambda` (in THz^2 x Angstrom^2)
+\mathbf{v}_\lambda` divided by primitive cell volume (in :math:`\text{THz}^2 /
+\text{Angstrom}`)
 
 ``--average``
 ^^^^^^^^^^^^^^
@@ -233,12 +234,12 @@ Modal heat capacity :math:`C_\lambda` (in eV/K)
 ^^^^^^^^^^^^^^
 
 Absolute value of group velocity :math:`|\mathbf{v}_\lambda|` (in
-THz x Angstrom)
+:math:`\text{THz}\cdot\text{Angstrom}`)
 
 ``--pqj``
 ^^^^^^^^^^^^^^
 
-Averaged phonon-phonon interaction :math:`P_{\mathbf{q}j}` (in eV^2)
+Averaged phonon-phonon interaction :math:`P_{\mathbf{q}j}` (in :math:`\text{eV}^2`)
 
 .. _auxiliary_tools_kdeplot:
 

doc/conf.py

@@ -165,6 +165,8 @@ html_theme_options = {
     # Choose Bootstrap version.
     # Values: "3" (default) or "2" (in quotes)
     'bootstrap_version': "3",
+
+    'nosidebar': "true",
 }
 
 

doc/hdf5_howto.rst

@@ -163,7 +163,7 @@ group_velocity
 ^^^^^^^^^^^^^^^
 
 Phonon group velocity, :math:`\nabla_\mathbf{q}\omega_\lambda`. The
-physical unit is :math:`\text{THz}\cdot\text{\AA}`, where THz
+physical unit is :math:`\text{THz}\cdot\text{Angstrom}`, where THz
 is in the ordinal frequency not the angular frequency.
 
 The array shape is (irreducible q-point, phonon band, 3 = Cartesian coordinates).
@@ -228,7 +228,7 @@ Outer products of group velocities for k-stars
    \mathbf{v}_{\mathbf{q}j}.
 
 The physical unit is
-:math:`\text{THz}^2\cdot\text{\AA}^2`, where THz is in the
+:math:`\text{THz}^2\cdot\text{Angstrom}^2`, where THz is in the
 ordinal frequency not the angular frequency.
 
 The array shape is (irreducible q-point, phonon band, 6 = (xx, yy, zz,
@@ -293,5 +293,3 @@ calculated by::
 
    kappa_unit_conversion / weight.sum() * heat_capacity[30, 2, 0] *
    gv_by_gv[2, 0] / (2 * gamma[30, 2, 0])
-
-

doc/interfaces.rst

@@ -42,8 +42,8 @@ unit systems used for the calculators are summarized below.
 
 Always (irrespective of calculator interface) the physical units of
 2nd and 3rd order force constants that are to be stored in
-``fc2.hdf5`` and ``fc3.hdf5`` are ``eV/Angstrom^2`` and
-``eV/Angstrom^3``, respectively.
+``fc2.hdf5`` and ``fc3.hdf5`` are :math:`\text{eV}/\text{Angstrom}^2` and
+:math:`\text{eV}/\text{Angstrom}^3`, respectively.
 
 .. _default_unit_cell_file_name_for_calculator:
 
@@ -70,4 +70,3 @@ Default displacement distances created by ``-d`` option without
    Pwscf   | 0.06 au (bohr)
    CRYSTAL | 0.03 Angstrom
    Abinit  | 0.06 au (bohr)
-

doc/output-files.rst

@@ -55,7 +55,7 @@ See the detail at :ref:`kappa_hdf5_file`.
 ^^^^^^^^^^^^^
 
 Third order force constants (in real space) are stored in
-:math:`\mathrm{eV}/\mathrm{\AA}^3`. 
+:math:`\mathrm{eV}/\text{Angstrom}^3`.
 
 In phono3py, this is stored in the numpy array ``dtype='double'`` and
 ``order='C'`` in the shape of::
@@ -109,7 +109,7 @@ So what you have to set is ``--pa="0 1/4 1/4  1/4 0 1/4  1/4 1/4 0"``.
 ^^^^^^^^^^^^^
 
 Second order force constants are stored in
-:math:`\mathrm{eV}/\mathrm{\AA}^3`.
+:math:`\mathrm{eV}/\text{Angstrom}^2`.
 
 In phono3py, this is stored in the numpy array ``dtype='double'`` and
 ``order='C'`` in the shape of::
@@ -149,5 +149,3 @@ Joint densities of states are stored in Thz. See :ref:`jdos_option`.
 
 ``linewidth-*.dat``
 ^^^^^^^^^^^^^^^^^^^^
-
-

doc/tips.rst

@@ -101,7 +101,7 @@ Displacement distance of atoms
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The phono3py default displacement distance is 0.03
-:math:`\text{\AA}`. In some cases, accurate result may not be obtained
+:math:`\text{Angstrom}`. In some cases, accurate result may not be obtained
 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

scripts/phono3py-kaccum

@@ -441,6 +441,8 @@ if __name__ == '__main__':
                                    mesh,
                                    ir_grid_points,
                                    grid_address)
+
+        # gv x gv is divied by primitive cell volume.
         unit_conversion = primitive.get_volume()
         mode_prop = gv_sum2.reshape((1,) + gv_sum2.shape) / unit_conversion
     else:
@@ -451,7 +453,7 @@ if __name__ == '__main__':
 
     frequencies = f['frequency'][:]
     conditions = frequencies > 0
-    if not conditions.all():
+    if conditions.sum() > 3:
         sys.stderr.write("# Imaginary frequencies are found. "
                          "They are set to be zero.\n")
         frequencies = np.where(conditions, frequencies, 0)