drprobe_interface

drprobe_interface provides a Python interface for using the command line tools of the Dr Probe software package.

Requirements

Dr Probe Command Line Tools must be installed.

Installation

pip install drprobe-interface

Example

The user is referred to the documentation of the Dr Probe command line tools for further information on S(TEM) image simulation. The following example provides a basic overview on the workflow of using the drprobe_interface package. A more detailled example for an HRTEM image simulation of SrTiO3 is given in the examples folder.

Import the drprobe_interface package:

import drprobe as drp

Run the celslc tool:

drp.commands.celslc(cel_file, slice_name, ht, *kwargs)

Create a msa-parameter file for the multislice algorithm:

msa_prm = drp.msaprm.MsaPrm()

Alternatively, you can also load an existing parameter file and edit it:

msa_prm = dr.msaprm.load_msa_prm('msa.prm')

You can edit the parameters of the file, for example the object tilt:

msa_prm.tilt_x = 1    # Applies 1° tilt in x-direction
msa_prm.tilt_y = 0.2  # Applies 0.2° tilt in y-direction

Then save the parameter file:

msa_prm.save_msa_prm('msa.prm')

Execute the multislice algorithm:

drp.commands.msa('msa.prm', 'output_name', *kwargs)

Create (or load) a wavimg-parameter file and edit the parameters accordingly, for example setting the output dimensions to 256 x 256 pixels. Afterwards, save the parameter file:

wavimg_prm = drp.wavimgprm.WavimgPrm()
wavimg_prm.output_dim = (256, 256)
wavimg_prm.output_files = 'img.dat'
wavimg_prm.save_wavimg_prm('wavimg.prm')

Simulate the image:

drp.commands.wavimg('wavimg.prm', *kwargs)

Depending on the datatype and size, the simulated image can be loaded in python using numpy:

import numpy as np
img = np.fromfile('img.dat', dtype='float32')
# Change dtype to 'complex64', when simulating complex-valued wavefunctions
img = img.reshape(wavimg_prm.output_dim)