Merge pull request #122 from romerogroup/dev

Dev

pyprocar/cfg/band_structure.yml

@@ -0,0 +1,101 @@
+spin_colors:
+  description: The colors for the plot lines.
+  value:
+  - blue
+  - red
+color:
+  description: The colors for the plot lines.
+  value: 'black'
+cmap:
+  description: The colormap used for the plot.
+  value: jet
+clim:
+    description: The color scale for the color bar
+    value: 
+    -
+    -
+fermi_color:
+  description: The color of the Fermi line.
+  value: blue
+fermi_linestyle:
+  description: The linestyle of the Fermi line.
+  value: dotted
+fermi_linewidth:
+  description: The linewidth of the Fermi line.
+  value: 1
+grid:
+  description: If true, a grid will be shown on the plot.
+  value: false
+grid_axis:
+  description: Which axis (or both) the grid lines should be drawn on.
+  value: both
+grid_color:
+  description: The color of the grid lines.
+  value: grey
+grid_linestyle:
+  description: The linestyle of the grid lines.
+  value: solid
+grid_linewidth:
+  description: The linewidth of the grid lines.
+  value: 1
+grid_which:
+  description: Which grid lines to draw (major, minor or both).
+  value: major
+label:
+  description: The labels for the plot lines.
+  value:
+  - $\uparrow$
+  - $\downarrow$
+legend:
+  description: If true, a legend will be shown on the plot.
+  value: true
+linestyle:
+  description: The linestyles for the plot lines.
+  value:
+  - solid
+  - dashed
+linewidth:
+  description: The linewidths for the plot lines.
+  value:
+  - 1.0
+  - 1.0
+marker:
+  description: The marker styles for the plot points.
+  value:
+  - o
+  - v
+  - ^
+  - D
+markersize:
+  description: The size of the markers for the plot points.
+  value:
+  - 0.2
+  - 0.2
+opacity:
+  description: The opacities for the plot lines.
+  value:
+  - 1.0
+  - 1.0
+plot_color_bar:
+  description: If true, a color bar will be shown on the plot.
+  value: true
+savefig:
+  description: The file name to save the figure. If null, the figure will not be saved.
+  value: null
+title:
+  description: The title for the plot. If null, no title will be displayed.
+  value: null
+weighted_color:
+  description: If true, the color of the lines will be weighted.
+  value: true
+weighted_width:
+  description: If true, the width of the lines will be weighted.
+  value: false
+figure_size:
+  description: The size of the figure (width, height) in inches.
+  value:
+  - 9
+  - 6
+dpi:
+  description: The resolution in dots per inch. If 'figure', use the figure's dpi value.
+  value: 'figure'

pyprocar/cfg/dos.yml

@@ -0,0 +1,136 @@
+cmap:
+  description: The colormap used for the plot.
+  value: jet
+colors:
+  description: List of colors for the plot lines.
+  value:
+  - red
+  - green
+  - blue
+  - cyan
+  - magenta
+  - yellow
+  - orange
+  - purple
+  - brown
+  - navy
+  - maroon
+  - olive
+fermi_color:
+  description: The color of the Fermi line.
+  value: black
+fermi_linestyle:
+  description: The linestyle of the Fermi line.
+  value: dotted
+fermi_linewidth:
+  description: The linewidth of the Fermi line.
+  value: 1
+figure_size:
+  description: The size of the figure (width, height) in inches.
+  value:
+  - 9
+  - 6
+font:
+  description: The font style for the plot text.
+  value: Arial
+font_size:
+  description: The size of the font used in the plot.
+  value: 16
+grid:
+  description: If true, a grid will be shown on the plot.
+  value: false
+grid_axis:
+  description: Which axis (or both) the grid lines should be drawn on.
+  value: both
+grid_color:
+  description: The color of the grid lines.
+  value: grey
+grid_linestyle:
+  description: The linestyle of the grid lines.
+  value: solid
+grid_linewidth:
+  description: The linewidth of the grid lines.
+  value: 1
+grid_which:
+  description: Which grid lines to draw (major, minor or both).
+  value: major
+legend:
+  description: If true, a legend will be shown on the plot.
+  value: true
+linestyle:
+  description: The linestyles for the plot lines.
+  value:
+  - solid
+  - dashed
+linewidth:
+  description: The linewidths for the plot lines.
+  value:
+  - 1
+  - 1
+marker:
+  description: The marker styles for the plot points.
+  value:
+  - o
+  - v
+  - ^
+  - D
+markersize:
+  description: The size of the markers for the plot points.
+  value:
+  - 0.2
+  - 0.2
+opacity:
+  description: The opacities for the plot lines.
+  value:
+  - 1.0
+  - 1.0
+plot_bar:
+  description: If true, a bar plot will be displayed.
+  value: true
+plot_color_bar:
+  description: If true, a color bar will be shown on the plot.
+  value: true
+plot_total:
+  description: If true, the total plot will be displayed.
+  value: true
+savefig:
+  description: The file name to save the figure. If null, the figure will not be saved.
+  value: null
+spin_colors:
+  description: The colors for the spin up and spin down lines.
+  value:
+  - black
+  - red
+spin_labels:
+  description: The labels for the spin up and spin down.
+  value:
+  - $\uparrow$
+  - $\downarrow$
+title:
+  description: The title for the plot. If null, no title will be displayed.
+  value: null
+verbose:
+  description: If true, the program will print detailed information.
+  value: true
+weighted_color:
+  description: If true, the color of the lines will be weighted.
+  value: true
+weighted_width:
+  description: If true, the width of the lines will be weighted.
+  value: false
+clim:
+  description: Value range to scale the colorbar
+  value:
+stack_y_label:
+  description: The label for the y-axis for stack mode
+  value: DOS
+x_label:
+  description: The label for the x-axis.
+  value: Energy (eV)
+y_label:
+  description: The label for the y-axis.
+  value: DOS
+dpi:
+  description: The resolution in dots per inch. If 'figure', use the figure's dpi value.
+  value: 'figure'
+

pyprocar/cfg/fermi_surface_2d.yml

@@ -0,0 +1,67 @@
+
+add_axes_labels:  
+  description: Boolean to add axes labels
+  value: true
+add_legend:  
+  description: Boolean to add legend
+  value: false
+plot_color_bar:
+  description: Boolean to plot the color bar
+  value: false
+
+
+cmap:  
+  description: The colormap used for the plot.
+  value: jet
+
+  value: jet
+clim:
+    description: The color scale for the color bar
+    value: 
+    -
+    -
+color:
+  description: The colors for the spin plot lines.
+  value:
+  - blue
+  - red
+linestyle:
+  description: The linestyles for the spin plot lines.
+  value:
+  - solid
+  - dashed
+linewidth:
+  description: The linewidth of the fermi surface
+  value: 0.2
+no_arrow:
+  description: Boolean to use no arrows to represent the spin texture
+  value: False
+
+arrow_color:
+  description: The linestyles for the spin plot lines.
+  value:
+
+arrow_density:
+  description: The arrow density for the spin texture
+  value: 10
+arrow_size:
+  description: The arrow size for the spin texture
+  value: 3
+arrow_projection:
+  description: The projection for the color scale for spin texture
+  value: z^2
+
+marker:
+  description: Controls the marker used for the spin plot
+  value: .
+dpi:
+  description: The dpi value to save the image as
+  value: figure
+
+x_label:
+  description: The x label of the plot
+  value: $k_{x}$  ($\AA^{-1}$)
+
+y_label:
+  description: The x label of the plot
+  value: $k_{y}$  ($\AA^{-1}$)

pyprocar/core/ebs.py

@@ -10,7 +10,7 @@
 # from . import Structure
 from typing import List
 import itertools
-
+import copy
 from scipy.interpolate import CubicSpline
 
 import numpy as np
@@ -637,13 +637,15 @@ def calculate_scalar_gradient(self,scalar_mesh):
         n_kz=len(np.unique(self.kpoints[:,2]))
         scalar_gradients =  np.zeros((3,n_kx,n_ky,n_kz))
 
-        if n_kx==1 or n_ky==1 or n_kz==1:
-            raise ValueError("The mesh cannot be 2 dimensional")
-
         # Calculate cartesian separations along each crystal direction
         sep_vectors_i = np.abs(self.kpoints_cartesian[self.index_mesh[[0]*n_kx, :, :], :] - self.kpoints_cartesian[self.index_mesh[[1]*n_kx, :, :], :])
         sep_vectors_j = np.abs(self.kpoints_cartesian[self.index_mesh[:, [0]*n_ky, :], :] - self.kpoints_cartesian[self.index_mesh[:, [1]*n_ky, :], :])
-        sep_vectors_k = np.abs(self.kpoints_cartesian[self.index_mesh[:, :, [0]*n_kz], :] - self.kpoints_cartesian[self.index_mesh[:, :, [1]*n_kz], :])
+
+        if n_kz>1:
+            sep_vectors_k = np.abs(self.kpoints_cartesian[self.index_mesh[:, :, [0]*n_kz], :] - self.kpoints_cartesian[self.index_mesh[:, :, [1]*n_kz], :])
+        else:
+            sep_vectors_k=copy.copy(sep_vectors_j)
+            sep_vectors_k[:,:,:,:]=0
 
         # Calculate indices with periodic boundary conditions
         plus_one_indices_x = np.arange(n_kx) + 1
@@ -669,6 +671,14 @@ def calculate_scalar_gradient(self,scalar_mesh):
         # Calculating gradients
         sep_vectors = [sep_vectors_i,sep_vectors_j,sep_vectors_k]
         energy_diffs = [scalar_diffs_i,scalar_diffs_j,scalar_diffs_k]
+
+        # Calculate gradients
+        # sep_vectors = [sep_vectors_i,sep_vectors_j]
+        # energy_diffs = [scalar_diffs_i,scalar_diffs_j]
+        # if n_kz > 1:  # Only add sep_vectors_k and scalar_diffs_k in 3D
+        #     sep_vectors.append(sep_vectors_k)
+        #     energy_diffs.append(scalar_diffs_k)
+
         for sep_vector,energy_diff in zip(sep_vectors,energy_diffs):
             for i_coord in range(3):
 
@@ -677,6 +687,9 @@ def calculate_scalar_gradient(self,scalar_mesh):
                 # Changing infinities to 0
                 tmp_grad = np.nan_to_num(tmp_grad, neginf=0,posinf=0) 
                 scalar_gradients[i_coord, :, :, :] += tmp_grad
+
+        if n_kz == 1:
+            scalar_gradients[2,:,:,:]=0
         return scalar_gradients
 
     def calculate_scalar_integral(self,scalar_mesh):