pybec.plotters.plot_BEC_v_spher

pybec.plotters.plot_BEC_v_spher(no_efield, clamped_ion, xyz, matrix_name, np_name, np_element, to_plot='r', centroid_of='all', e_field=0.001, e_field_direction=[0, 0, 1], cmap=None, cbar_pos='top', legend=True, figsize=(8, 4), marker_dict=None, color_dict=None, grid=False, alpha=1.0, cbar_shrink=1.0)[source]

Plots the Born Effective Charges for each ion against the distance of that ion from the nanoparticle centroid.

Parameters

  • no_efield (str) – File path to the zero field step output file

  • clamped_ion (str) – File path to the clamped ion step output file

  • xyz (str) – File path to the optimized structure .xyz file

  • matrix_name (str) – Whatever you want to call the matrix, e.g. ‘MgO’

  • np_name (str) – Whatever you want to call the mNP, e.g. ‘Ag8_333’

  • np_element (str) – Elemental symbol for nanoparticle element.

  • centroid_of (str, optional) – The element you want to calculate the centroid for when calculating and plotting against the distance to centroid. If ‘all’, it will calculate the centroid of the whole unit cell. ‘Ag’ will calculate the centroid of all silver ions in the unit cell in the relaxed structure. Default: ‘all’

  • e_field (float, optional) – The electric field in au. Default: 0.001

  • e_field_direction (int, optional) – The direction the field is applied, where the x-axis is [1,0,0], y-axis is [0,1,0], and z-axis is [0,0,1]. Default: [0,0,1]

  • cmap (string, optional) – The matplotlib colormap style used to color the absolute value of their Born Effective Charge. If None, the data instead will be colored by element using the color_dict colors or default matplotlib ones. Default: None

  • cbar_pos (str, optional) – Where to place the colorbar if cmap is used. Can be ‘top’, ‘right’, or ‘bottom’. Default: ‘top’

  • legend (bool, optional) – Whether to include a legend labelling the different elements. Default: True

  • figsize ((int, int), optional) – Width, Height of the figure. Default: (8,4)

  • marker_dict (dict, optional) – Custom dictionary specifying which markers to use for each element, where the keys are element symbols and the values are valid matplotlib marker symbols. Default: None Ex: {‘O’: ‘o’, ‘Ag’: ‘x’, ‘Mg’: ‘>’}

  • color_dict (dict, optional) – Custom dictionary specifying which colors to use for each element, where the keys are element symbols and the values are valid matplotlib color symbols. Default: None Ex: {‘O’: ‘r’, ‘Ag’: ‘k’, ‘Mg’: ‘y’}

  • grid (bool, optional) – Whether to include grid lines in the plot. Default: False

  • alpha (float) – The alpha channel value for the plot colors. Default: 1.0

Returns

Return type

None