1.2.2. CAVD calculations

1. Introduction

      CAVD (Crystal structure Analysis by Voronoi Decomposition) is an high-throughput tool that towards better characterization of void space for ionic transport analysis.
      Using CAVD, the void space inside ionic crystal can be characterized as the 3D network consisting of interstices, channels between interstices, and bottlenecks of the channels, which are identified and quantified from the position and geometry of Voronoi polyhedra vertices, edges, and faces, respectively. The geometric and topological parameters of the network are then translated into ion transport descriptors. These descriptors form the foundation of machine-learning algorithms to predict and optimize materials properties.

2. Step-by-Step Guide

   Create a computing task following the steps below

   

   Fig. 1.6 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

     • You can upload a single cif structure file (with valence information) or pack multiple cif structure files (up to 50) into a zip format compression package for upload.

     • 除迁移离子外的其他离子位点占据率需为1的cif结构文件。示例文件

   • Computing parameters

     Parameter name	Parameter type	Description
     Migration Ion	String	Element names of migration Ion
     distance tolerance	Float	Unit:Å The default value is 0.002Å, to control the precision of the boundaries and faces generated in the Voronoi diagram
     radius flag	Bool	The default value is True, indicating the use of the Voronoi decomposition algorithm considering radii
     lower threshhold of ion-migration	Float	the lower threshold of ion migration to select the suitable interstitial network, with a default value of 0.0
     upper threshhold of ion-migration	Float	the upper threshold of ion migration to select the suitable interstitial network, with a default value of 10.0

   • Running Parameters

     Currently no need to set, keep the default settings.

     Parameter name	Parameter type	Description
     Machine Name	String	Machine name, default is machine01
     Number of Core	Positive integer	Number of Compute cores, default is 1
     Number of Process	Positive integer	Number of Computing processes, default is 1

4. Computational Result Files

   • *_origin.ner: The network of interstices for migrations ions,preserving the bottlenecks, interstice positions, and geometric dimensions within the interstice network.

   • *.net:The interstice network of migrating ions given lower and upper bounds.Consistent with the *_origin.net file forma

   • *.vesta: The interstice network visualization file, which can be visualized using VESTA software

   • *.resex: Contains complete information about the connectivity status