Introduction

1. Goal

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This program is designed to carry out a thorough search of all possible bonding locations for a new single atom to the atoms of any 2D or 3D material models with a given target bondlength, and to generate the calculation seed files accordingly. 

This program aims to conduct a rational, rapid, consistent and comprehensive model building workflow to free the computational chemistry scientists from the laborious efforts of creating possible adsorbate-surface interaction models by hands. 

This program is mathematically designed to generate positions with high accuracy and consistency. It also efficiently identifies multi-coordinated positions based on specified bond lengths and generates potential configurations for singly and doubly coordinated sites while minimizing unwanted interactions with surrounding atoms. Therefore, it naturally fits the demand of big data analysis in computational chemistry, as those massive amounts of data source from the massive amounts of material model inputs!

 

2. Background and Algorithm

The possibilities of available adsorption sites on a catalyst surface is enormous. Screening for it requires a large number of modelings in computations. Building models for such tasks are excessively laborious for human-beings, especially when accuracy is taken into account. Therefore, we envisaged accomplishing it with aid of programming. However, it is adding a new node to an existing network of nodes with a strictly defined distance, which can only find a few references in geotopical programming. In addition, considering the 3-dimensional nature of our problem, the experience in that 2-dimensional topics is hard to transfer into our issue. As a result, we had to think outside the box and start from scratch.