Minor fixes

phonopy/__init__.py

@@ -492,7 +492,7 @@ class Phonopy:
     def write_yaml_mesh(self):
         self._mesh.write_yaml()
 
-    def plot_band_structure_and_dos(self, symbols=None):
+    def plot_band_structure_and_dos(self, pdos_indices=None, symbols=None):
         import matplotlib.pyplot as plt
         import matplotlib.gridspec as gridspec
         if symbols:
@@ -506,10 +506,18 @@ class Phonopy:
         ax2 = plt.subplot(gs[0, 1], sharey=ax1)
         plt.subplots_adjust(wspace=0.03)
         plt.setp(ax2.get_yticklabels(), visible=False)
+
+        if pdos_indices is None:
             self._total_dos.plot(plt,
                                  ylabel="",
                                  draw_grid=False,
                                  flip_xy=True)
+        else:
+            self._pdos.plot(plt,
+                            indices=pdos_indices,
+                            ylabel="",
+                            draw_grid=False,
+                            flip_xy=True)
 
         return plt
 

phonopy/phonon/dos.py

@@ -100,9 +100,6 @@ def plot_partial_dos(pyplot,
                      ylabel=None,
                      draw_grid=True,
                      flip_xy=False):
-    pyplot.grid(draw_grid)
-    pyplot.xlabel('Frequency')
-    pyplot.ylabel('Partial density of states')
     plots = []
 
     num_atom = len(partial_dos)
@@ -119,11 +116,21 @@ def plot_partial_dos(pyplot,
                 print "Your specified atom number is out of range."
                 raise ValueError
             pdos_sum += partial_dos[i]
+        if flip_xy:
+            plots.append(pyplot.plot(pdos_sum, frequency_points))
+        else:
             plots.append(pyplot.plot(frequency_points, pdos_sum))
 
     if legend is not None:
         pyplot.legend(legend)
 
+    if xlabel:
+        pyplot.xlabel(xlabel)
+    if ylabel:
+        pyplot.ylabel(ylabel)
+
+    pyplot.grid(draw_grid)
+    
 class NormalDistribution:
     def __init__(self, sigma):
         self._sigma = sigma
@@ -366,12 +373,36 @@ class PartialDos(Dos):
         """
         return self._frequency_points, self._partial_dos
 
-    def plot(self, pyplot, indices=None, legend=None):
+    def plot(self,
+             pyplot,
+             indices=None,
+             legend=None,
+             xlabel=None,
+             ylabel=None,
+             draw_grid=True,
+             flip_xy=False):
+
+        if flip_xy:
+            _xlabel = 'Partial density of states'
+            _ylabel = 'Frequency'
+        else:
+            _xlabel = 'Frequency'
+            _ylabel = 'Partial density of states'
+
+        if xlabel is not None:
+            _xlabel = xlabel
+        if ylabel is not None:
+            _ylabel = ylabel
+
         plot_partial_dos(pyplot,
                          self._frequency_points,
                          self._partial_dos,
                          indices=indices,
-                         legend=legend)
+                         legend=legend,
+                         xlabel=_xlabel,
+                         ylabel=_ylabel,
+                         draw_grid=draw_grid,
+                         flip_xy=flip_xy)
     
     def write(self):
         if self._tetrahedron_mesh is None:

scripts/bandplot

@@ -221,9 +221,9 @@ if not options.is_gnuplot:
     
     plt.xlim(distances[0], distances[-1])
     if options.f_max is not None:
-        plt.ylim(ymax = options.f_max)
+        plt.ylim(ymax=options.f_max)
     if options.f_min is not None:
-        plt.ylim(ymin = options.f_min)
+        plt.ylim(ymin=options.f_min)
     plt.axhline(y=0, linestyle=':', linewidth=0.5, color='b')
     if len(filenames) == 1:
         xticks = segment_positions + [distances[-1]]
@@ -251,6 +251,10 @@ if not options.is_gnuplot:
         plt.setp(ax2.get_yticklabels(), visible=False)
         plt.plot(dos, dos_frequencies)
         plt.xlabel('DOS')
+        if options.f_max is not None:
+            plt.ylim(ymax=options.f_max)
+        if options.f_min is not None:
+            plt.ylim(ymin=options.f_min)
     
     if options.output_filename is not None:
         plt.rcParams['pdf.fonttype'] = 42

scripts/phonopy

@@ -1012,13 +1012,12 @@ elif run_mode == 'band' or run_mode == 'mesh' or run_mode == 'band_mesh':
     
         # Partial DOS
         elif (settings.get_is_eigenvectors() and
-              (options.is_graph_plot or settings.get_is_dos_mode()) and
+            (options.is_graph_plot or settings.get_is_dos_mode())):
-              (not settings.get_is_thermal_properties())):
             p_direction = settings.get_projection_direction()
             if log_level > 0:
                 if p_direction is not None:
                     print "Projection direction:", np.array(p_direction)
-                print "Calculating PDOS..."
+                print "Calculating partial DOS..."
             dos_range = settings.get_dos_range()
             phonon.set_partial_DOS(
                 sigma=settings.get_sigma(),
@@ -1032,7 +1031,10 @@ elif run_mode == 'band' or run_mode == 'mesh' or run_mode == 'band_mesh':
             if options.is_graph_plot:
                 pdos_indices = settings.get_pdos_indices()
                 if pdos_indices is None:
-                    pdos_indices = [range(primitive.get_number_of_atoms())]
+                    pdos_indices = [[x] for x in
+                                    range(primitive.get_number_of_atoms())]
+
+            if options.is_graph_plot and run_mode != 'band_mesh':
                 plot = phonon.plot_partial_DOS(
                     pdos_indices=pdos_indices,
                     legend=([np.array(x) + 1 for x in pdos_indices]))
@@ -1069,7 +1071,17 @@ elif run_mode == 'band' or run_mode == 'mesh' or run_mode == 'band_mesh':
                 else:
                     plot.show()
 
-        if options.is_graph_plot and run_mode == 'band_mesh':
+    if (run_mode == 'band_mesh' and
+        options.is_graph_plot and
+        not settings.get_is_thermal_properties() and
+        not settings.get_is_thermal_displacements() and
+        not settings.get_is_thermal_displacement_matrices() and
+        not settings.get_is_thermal_distances()):
+        if settings.get_is_eigenvectors():
+            plot = phonon.plot_band_structure_and_dos(
+                pdos_indices=pdos_indices,
+                symbols=settings.get_band_labels())
+        else:
             plot = phonon.plot_band_structure_and_dos(
                 symbols=settings.get_band_labels())
         if options.is_graph_save: