README.md

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This tutorial is written by Toon Verstraelen for students of the course "Elektriciteit, Magnetisme en Sensoren" (I002429) of the B.Sc. Bioscience Engineering at Ghent University.

Computational Tutorial Electromagnetism: charge distributions in copper nanostructures

Overview

This repository contains two Jupyter notebooks:

• 1_slice_of_numpy.ipynb: a crash course on NumPy for absolute beginners. It does not attempt to give a complete introduction to NumPy. Instead, it covers only the basics needed to work on the second notebook.
• 2_charge_nano.ipynb: the assignment to be solved.

How to get started.

• You can open the notebooks with Google Colab using the following links:

  • 1_slice_of_numpy.ipynb on Google Colab
  • 2_charge_nano.ipynb on Google Colab

  The second notebook needs additional data files. One of the code cells in the notebook can be used to download them into your runtime on Colab.

• You can also work with the notebooks locally by downloading this repository as a ZIP file and unzipping it on your computer. You can then open the notebooks using Jupyter Lab or VSCode.

Theory recap

The charge model in this tutorial is a flavor of electronegativity equalization or charge equilibration. Although this model was originally proposed to calculate charge distributions in organic molecules, it is better suited to describe metallic systems. The energy as a function of the charges has the form:

$$ U = \sum_{i=1}^N B_i q_i + \frac{1}{2} \sum_{i=1}^N \sum_{j=1}^N q_i A_{ij} q_j $$

with

$$\begin{aligned} B_i &= \chi \\ A_{ij} &= \begin{cases} \eta & \text{if $i=j$} \\ \frac{1}{4\pi\epsilon_0 \left\Vert \vec{R}_i - \vec{R}_j \right\Vert} & \text{if $i \neq j$} \end{cases} \end{aligned}$$

where $q_i$ are atomic partial charges and $\vec{R}_i$ are the particle positions. The electronegativity $\chi$ and hardness $\eta$ are constant model parameters. In this tutorial, we'll assume elemental systems, so all atoms have the same parameters.

The off-diagonal second-order terms represent the Coulumb interaction between point charges. To obtain a positive definite potential energy expression and to make the model a bit more realistic, we will use a damped electrostatic interaction instead:

$$ A_{ij} = \frac{1 - \exp(-r_{ij}/\sigma)}{4\pi \epsilon_0, r_{ij}} $$

It can be shown that the energy is positive definite for any configuration of the atoms when $\eta > 1 / 4 \pi \epsilon_0 \sigma$.

The minimizer of the energy with a fixed total charge corresponds to the stationary point of the following Lagrangian:

$$ L = U + \lambda \left(\sum_{i=1}^N q_i - q_\text{tot}\right) $$

The ground-state charge distribution is therefore found by solving the following system of linear equations:

$$ \begin{bmatrix} A_{11} & A_{12} & \cdots & A_{1N} & 1 \\ A_{21} & A_{22} & \cdots & A_{2N} & 1 \\ \vdots & \vdots & \ddots & \vdots & \vdots \\ A_{N1} & A_{N2} & \cdots & A_{NN} & 1 \\ 1 & 1 & \cdots & 1 & 0 \end{bmatrix} \begin{bmatrix} q_1 \\ q_2 \\ \vdots \\ q_N \\ \lambda \end{bmatrix} = \begin{bmatrix} \chi \\ \chi \\ \vdots \\ \chi \\ q_\text{tot} \end{bmatrix} $$