1.4.2. Similar Structure Identification

1. Introduction

   To identify similar crystal structures, additional comparison criteria can be incorporated, including atomic type, atomic occupancy, atomic oxidation state, and atomic magnetic moment. If a specific comparison criterion is chosen, it would be taken into account during similarity calculations.

2. Step-by-Step Guide

   Create a computing task following the steps below

   

   Fig. 1.15 computational_workflow

   
   

   • step 1. Create a new task: Enter the name and description of the computing task on the corresponding page, click the “OK” button to complete the creation of the computing task; click the “Cancel” button to clear the input content

   • step 2. Upload files: Follow the instructions on the corresponding page to upload computing input files.

     Attention:

     • Please make sure to name computing input files in English!

     • If you need to upload multiple computation input files, please compress them into a zip file and upload the zip file.

   • step 3. Set computation parameters: Set computation parameters according to the prompts on the corresponding page.

   • step 4. Set runtime parameters: Currently, no need to set runtime parameters, keep the input box at default settings.

   • step 5. Save computation task: Complete the creation of the computation task and add it to the computation project. On the redirected page, you can choose

     • Continue adding computation tasks: Add a new computation task

     • View Project: View details of the current pending computational project

3. Parameter description

   • Input File

     • Please upload a compressed file containing at least two CIF files, named in English

     • 示例文件

   • Computing Parameters

     Parameters Name	Parameters Type	Description
     Atomic Type	Bool[True（1）,False（0）]	Whether atomic types on the site are considered, False (0) is not considered
     atomic occupancy	Bool[True（1）,False（0）]	Whether atomic occupancies on the site are considered, False (0) is not considered
     atomic oxidation state	Bool[True（1）,False（0）]	Whether atomic oxidation state on the site are considered, False (0) is not considered
     atomic magnetic moment	Bool[True（1）,False（0）]	Whether atomic magnetic moment on the site are considered, False (0) is not considered
     Similarity threshold	Float（Float）	default to 0.9, used to determine similarity

   • Running Parameters：

     Currently no need to set, keep the default settings.

     Parameters Name	Parameters Type	Description
     Machine Name	String（String）	Machine name, default is machine01
     Number of Core	Positive integer（Int）	Number of Compute cores, default is 1
     Number of Process	Positive integer（Int）	Number of Computing processes, default is 1

4. Computational Result Files

   After the calculation is completed, a CSV format file will be obtained, and the meaning of each column in the CSV format file is

   • filename:Crystal structure file name

   • similar_group_id:Similar structure group number (In the function of identifying similar structures, if the crystal structure has the same group number, it is recognized as having a similar structure after comparing the structure framework with the selected comparison criteria)

   • similarity:Similarity value, the similarity between the first structure in the same similar structure group

   • same_group_id:Same structure group number (In the function of identifying the same structure, if the crystal structure has the same group number, it means that after comparing the structure framework, atomic type, and atomic occupancy rate, the crystal is recognized as having the same structure)