Merge pull request #48 from nanotech-empa/release/1.4.2

Release/1.4.2

nanoribbon/viewers/show_computed.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Viewers to display the results of the Nanoribbon work chain."""
 
 # Base imports.
@@ -387,6 +388,8 @@ def __init__(self, cmap='seismic', center0=True, show_cbar=True, export_label=No
                                                  continuous_update=False,
                                                  layout=layout)
         self.height_slider.observe(self.update_plot, names='value')
+        self.selected_height = 0.0 # angstrom
+
         self.opacity_slider = ipw.FloatSlider(description="Opacity",
                                               value=0.5,
                                               max=1.0,
@@ -454,14 +457,16 @@ def update_axis(self, _=None):
 
         geo_center = np.sum(self._current_structure.positions, axis=0) / len(self._current_structure)
 
-        z_arr = np.array([d_z * i - geo_center[2] for i in range(0, n_z, 1)])
-        i_closest_to_1ang = (np.abs(z_arr - 1.0)).argmin()
+        self.z_arr = np.array([d_z * i - geo_center[2] for i in range(0, n_z, 1)])
 
-        for i, z in enumerate(z_arr):
+        for i, z in enumerate(self.z_arr):
             options[u"{:.3f} Å".format(z)] = i
 
         self.height_slider.options = options
-        self.height_slider.value = list(options.values())[i_closest_to_1ang]
+
+        i_start = (np.abs(self.z_arr - 2.5)).argmin()
+        self.height_slider.value = list(options.values())[i_start]
+        self.selected_height = self.z_arr[i_start]
 
     def update_plot(self, _=None):
         """Update the 2D plot with the new data."""
@@ -470,6 +475,7 @@ def update_plot(self, _=None):
             fig, axplt = plt.subplots()
             fig.dpi = 150.0
             data = self._current_data[:, :, self.height_slider.value]
+            self.selected_height = self.z_arr[self.height_slider.value]
             flipped_data = np.flip(data.transpose(), axis=0)
 
             vmax = np.max(flipped_data) * self.colormap_slider.value
@@ -530,9 +536,11 @@ def make_export_link_txt(self, data):
         enc_file = b64encode(tempio.getvalue()).decode()
 
         if self.export_label is not None:
-            filename = "{}.txt".format(self.export_label)
+            plot_name = self.export_label
         else:
-            filename = "export.txt"
+            plot_name = "export"
+
+        filename = "{}_h{:.3f}.txt".format(plot_name, self.selected_height)
 
         html = '<a download="{}" href="'.format(filename)
         html += 'data:chemical/txt;name={};base64,{}"'.format(filename, enc_file)
@@ -546,7 +554,8 @@ def make_export_link_igor(self, data):
             plot_name = self.export_label
         else:
             plot_name = "export"
-        filename = plot_name + ".itx"
+
+        filename = "{}_h{:.3f}.itx".format(plot_name, self.selected_height)
 
         igorwave = Wave2d(
                 data=data,
@@ -634,7 +643,11 @@ def __init__(self, workcalc, **kwargs):
         ]
         custom_cmap = matplotlib.colors.LinearSegmentedColormap.from_list("half_seismic", custom_cmap_colors)
 
-        self.orbital_viewer_2d = CubeArrayData2dViewerWidget(cmap=custom_cmap, center0=False, export_label="pk%d_orbital" % workcalc.pk)
+        self.orbital_viewer_2d = CubeArrayData2dViewerWidget(
+            cmap=custom_cmap,
+            center0=False,
+            export_label=None
+        )
         self.orbital_viewer_3d = CubeArrayData3dViewerWidget()
 
         self.info_out = ipw.HTML()
@@ -766,7 +779,14 @@ def on_kpoint_change(self, _=None):
             arraydata, fname = arraydata_fn
             self.info_out.value = fname
 
+            self.orbital_viewer_2d.export_label = "pk{}_b{}_k{:02}_s{}".format(
+                self._workcalc.pk,
+                self.bands_viewer.selected_band,
+                self.bands_viewer.selected_kpoint,
+                self.bands_viewer.selected_spin,
+            )
             self.orbital_viewer_2d.arraydata = self.clamp_arraydata_to_zero(arraydata)
+
             with self.output:
                 clear_output()                        
                 if self.bands_viewer.selected_3D:
@@ -835,6 +855,10 @@ def on_sts_btn_click(self, _=None):
                 ]
             else:
                 self.sts_mapping_viewer_wrapper.children = [self.sts_mapping_viewer]
+
+            self.sts_mapping_viewer.export_label = "pk{}_ldos_fwhm{}_e{}".format(
+                self._workcalc.pk, self.sts_fwhm_text.value, self.sts_energy_text.value
+            )
             self.sts_mapping_viewer.arraydata = sts_arraydata
         else:
             self.sts_mapping_viewer_wrapper.children = [ipw.HTML(value="Could not find data.")]

setup.cfg

@@ -3,7 +3,7 @@ title = Empa nanotech@surfaces Laboratory - Graphene nanoribbons
 
 [metadata]
 name = nanoribbons
-version = 1.4.1
+version = 1.4.2
 author = nanotech@surfaces laboratory, Empa
 description = Tools for graphene nanoribbons, developed at the nanotech@surfaces laboratory, Empa
 long_description = file: README.md

show.ipynb

@@ -53,7 +53,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },