--zmax option is made for kdeplot.

doc/auxiliary-tools.rst

@@ -233,9 +233,9 @@ higher lifetime side is not drawn if all density beyond a lifetime
 value is smaller than some ratio (see
 :ref:`kdeplot_density_ratio`) of the maximum density.
 
-The following plot is drawn with a
-19x19x19 mesh and nbins=200 and the ``Si-PBEsol`` example is used to
-generate the data.
+The following plot is drawn with a 19x19x19 mesh and nbins=200 and the
+``Si-PBEsol`` example is used to generate the data. The colormap of
+'jet' in matplotlib is used.
 
 .. |ikde| image:: Si-kdeplot.png
         :width: 50%
@@ -295,19 +295,15 @@ computation will be roughly twice faster.
 
    % kdeplot --ymax=60 kappa-m111111.hdf5
 
-``--cmap``
+``--zmax``
 ^^^^^^^^^^^
 
 **New**: The latest version of ``kdeplot`` is download at
 https://github.com/atztogo/phono3py/blob/develop/scripts/kdeplot.)
 
-Color map to be used for the density plot. It's given by the name
-presented at the matplotlib documentation,
-https://matplotlib.org/users/colormaps.html.
-
-::
-
-   % kdeplot --cmap="OrRd" kappa-m111111.hdf5
+Maximum value of the density is specified with this option. The color
+along colorbar saturates by choosing a smaller value than the maximum value
+of density in the data.
 
 .. _kdeplot_density_ratio:
 
@@ -325,3 +321,38 @@ together, this option is ignored.
 ::
 
    % kdeplot --dr=0.01 kappa-m111111.hdf5
+
+``--cmap``
+^^^^^^^^^^^
+
+**New**: The latest version of ``kdeplot`` is download at
+https://github.com/atztogo/phono3py/blob/develop/scripts/kdeplot.)
+
+Color map to be used for the density plot. It's given by the name
+presented at the matplotlib documentation,
+https://matplotlib.org/users/colormaps.html. The default colormap
+depends on your matplotlib environment.
+
+::
+
+   % kdeplot --cmap="OrRd" kappa-m111111.hdf5
+
+The following figures are those drawn with ``jet``, ``bwr``,
+``seismic``, ``gnuplot``, ``hsv``, and ``OrRd`` colormaps. 
+
+
+.. |ikde-jet| image:: Si-kdeplot-jet.png
+	      :width: 25%
+.. |ikde-bwr| image:: Si-kdeplot-bwr.png
+	      :width: 25%
+.. |ikde-seismic| image:: Si-kdeplot-seismic.png
+		  :width: 25%
+.. |ikde-gnuplot| image:: Si-kdeplot-gnuplot.png
+		  :width: 25%
+.. |ikde-hsv| image:: Si-kdeplot-hsv.png
+	       :width: 25%
+.. |ikde-OrRd| image:: Si-kdeplot-OrRd.png
+	       :width: 25%
+
+|ikde-jet| |ikde-bwr| |ikde-seismic| |ikde-gnuplot| |ikde-hsv| |ikde-OrRd|
+

scripts/kdeplot

@@ -76,7 +76,7 @@ def run_KDE(x, y, nbins, x_max=None, y_max=None, density_ratio=0.1):
     return xi, yi, zi, short_nbinds
 
 def plot(plt, xi, yi, zi, x, y, short_nbinds, nbins,
-         y_max=None, cmap='viridis'):    
+         y_max=None, z_max=None, cmap=None):    
     #
     # Plotting
     #
@@ -92,7 +92,8 @@ def plot(plt, xi, yi, zi, x, y, short_nbinds, nbins,
             y_cut.append(_y)
     
     fig = plt.figure()
-    plt.pcolormesh(xi[:,:nbins], yi[:,:nbins], zi[:,:nbins], cmap=cmap)
+    plt.pcolormesh(xi[:,:nbins], yi[:,:nbins], zi[:,:nbins],
+                   vmax=z_max, cmap=cmap)
     plt.colorbar()
     
     plt.scatter(x_cut, y_cut, s=5, c='k', marker='.', linewidth=0)
@@ -112,7 +113,7 @@ def plot(plt, xi, yi, zi, x, y, short_nbinds, nbins,
 # Arg-parser
 parser = argparse.ArgumentParser(
     description="Plot property density with gaussian KDE")
-parser.add_argument("--cmap", dest="cmap", default="viridis",
+parser.add_argument("--cmap", dest="cmap", default=None,
                     help="Matplotlib cmap")
 parser.add_argument("--cutoff",
                     help=("Property (y-axis) below this value is included in "
@@ -124,6 +125,9 @@ parser.add_argument("--dr", "--density_ratio", dest="density_ratio",
                     type=float, default=0.1)
 parser.add_argument("--fmax", help="Max frequency to plot",
                     type=float, default=None)
+parser.add_argument('--gv_norm', action='store_true',
+                    help=("|gv| is used for the density plot instead of "
+                          "lifetime.")),
 parser.add_argument('--nbins', type=int, default=100,
                     help=("Number of bins in which data are assigned, "
                           "i.e., determining resolution of plot")),
@@ -138,6 +142,9 @@ parser.add_argument("--xmax",
 parser.add_argument("--ymax",
                     help="Set maximum y of draw area",
                     type=float, default=None)
+parser.add_argument("--zmax",
+                    help="Set maximum indisity",
+                    type=float, default=None)
 parser.add_argument('filenames', nargs='*')
 args = parser.parse_args()
 
@@ -189,15 +196,20 @@ print("Temperature at which lifetime density is drawn: %7.3f"
 #
 weights = f['weight'][:]
 frequencies = f['frequency'][:]
-gammas = [f['gamma'][t_index],]
 symbols = ['',]
-if args.nu:
-    if 'gamma_N' in f:
-        gammas.append(f['gamma_N'][t_index])
-        symbols.append('N')
-    if 'gamma_U' in f:
-        gammas.append(f['gamma_U'][t_index])
-        symbols.append('U')
+
+if args.gv_norm:
+    gv_norm = np.sqrt((f['group_velocity'][:, :, :] ** 2).sum(axis=2))
+    gammas = [gv_norm,]
+else:
+    gammas = [f['gamma'][t_index],]
+    if args.nu:
+        if 'gamma_N' in f:
+            gammas.append(f['gamma_N'][t_index])
+            symbols.append('N')
+        if 'gamma_U' in f:
+            gammas.append(f['gamma_U'][t_index])
+            symbols.append('U')
 
 #
 # Run
@@ -210,7 +222,7 @@ for gamma, s in zip(gammas, symbols):
                                        y_max=args.ymax,
                                        density_ratio=args.density_ratio)
     fig = plot(plt, xi, yi, zi, x, y, short_nbinds, args.nbins,
-               y_max=args.ymax, cmap=args.cmap)
+               y_max=args.ymax, z_max=args.zmax, cmap=args.cmap)
     if s:
         fig.savefig("lifetime-%s.png" % s)
     else: