Welcome to the Adsorber documentation!

Section author: Geoffrey Weal <geoffrey.weal@gmail.com>

Section author: Dr. Anna Garden <anna.garden@otago.ac.nz>

Group page: https://blogs.otago.ac.nz/annagarden/

What is Adsorber

Adsorber is a program designed to adsorb molecules in various way to the surface of a cluster or a surface. This program adsorbed molecules ontop of atoms, ontop of bridge sites, ontop of three-fold sites, and ontop of four fold sites.

A guide on how to use the Adsorber program is given in Guide To Using Adsorber.

This program is definitely a “work in progress”. I have made it as easy to use as possible, but there are always oversights to program development and some parts of it may not be as easy to use as it could be. If you have any issues with the program or you think there would be better/easier ways to use and implement things in Adsorber, feel free to email Geoffrey about these (geoffrey.weal@gmail.com). Feedback is very much welcome!

Installation

It is recommended to read the installation page before using the Adsorber program. See Installation: Setting Up Adsorber and Pre-Requisites Packages for more information. Note that you can install Adsorber through pip3 and conda.

As well as installing Adsorber, the Atomic Simulation Environment (ASE) GUI and Jmol programs are also used to visualise your system with adsorbed atoms and molecules upon it. Installation and how to use the ASE GUI and Jmol can be found in External Programs that will be useful to install for using Adsorber.

Guide To Using Adsorber

After you have installed Adsorber and all other helpful programs, see Guide To Using Adsorber to learn about the process of using Adsorber to obtain models of your system with various adsorbates for further optimisation with VASP.

Table of Contents

• Installation: Setting Up Adsorber and Pre-Requisites Packages
  • Pre-requisites
  • Setting up Adsorber
  • Visualisation Programs for looking at systems with adsorbed molecules
  • Other Useful things to know before you start
  • Summary of what you want in the ~/.bashrc for the LatticeFinder program if you manually installed LatticeFinder
• External Programs that will be useful to install for using Adsorber
  • ASE GUI (from Atomic Simulation Environment)
  • Jmol
• Guide To Using Adsorber
  • Prelude Step
  • Part A
  • Part B
  • Part C
  • Part D
  • Final Notes about this process
• Prelude 1: Setting your general.py and adsorbate.py scripts
  • Setting your general.py scripts
  • Setting your adsorbate.py scripts
• Prelude 2: How to obtain some of the settings for the adsorber.py script
  • How to Bind Molecule to the Surface of your Cluster/Surface Model in Adsorber
• Part A: How to optimise your system, as well as optimise adsorbates and other molecules
  • Setting up the partA.py input script
  • Other files you need: The VASP_Files folder
  • Run Adsorber PartA
  • What will Adsorber do?
  • What do you need to do?
  • Note regarding surface models
• Part B1: Adsorbing Adsorbates to your System
  • Setting up the partB.py input script
  • Run Adsorber PartB
  • What will Adsorber do?
  • What do you need to do?
• Part B1: How to Mark Surface Atoms in your Cluster/Surface model in Adsorber
• Part B2: How to choose which xyz files to optimise in VASP
  • How to choose which xyz files to optimise in VASP
  • Selecting binding sites using the Label command in Jmol
  • Advice on how I Choose xyz Files for VASP Optimise with Adsorber
  • How to automate the copying of these xyz files: Using copy_files_from_folder_B_to_C.py
  • What To Do Once You Have Placed Selected xyz Files Into Part_C_Selected_Systems_with_Adsorbed_Species_to_Convert_into_VASP_files
• Part C1: Preparing Selected Adsorbed Systems For VASP Optimisation
  • Setting up the partC.py input script
  • Other files you need: The VASP_Files folder
  • Run Adsorber PartC
  • What will Adsorber do?
  • What do you need to do?
  • What to do if you made a mistake that you want to fix before submitting VASP jobs to slurm
• Part C1: How to submit VASP jobs to Slurm: Adsorber submit
  • Adsorber submit settings that can be changed
  • Adsorber check_submit: Other useful commands to see how many jobs are running and the number of jobs that you will submit
  • A command to determine the number of jobs you have already running in slurm
  • What to do if some jobs need to be resubmit for some reason
• Part C2: What To Do If Some Jobs Have Not Finished/Converged
  • Adsorber check_unconverged: Determine which jobs have converged and which have not
  • What to do if you want to resubmit jobs to slurm
  • What should I do if I do not want to use prepare_unconverged_VASP_jobs.py to prepare jobs for resubmission but want to just resubmit certain jobs: Adsorber prep_single_resub
  • What to do if some of my calculations are not converging and you want to repeat them from the beginning: Adsorber repeat
  • What to do when you are ready to resubmit VASP jobs to slurm
• Part D: Gathering Information from VASP Calculations
  • What do you need to do?
• Part D: Supplementary Methods
  • Adsorber compare: Comparing systems where adsorbate binds to the same surface atoms
  • Adsorber tidy: Clean up the files for jobs that you are happy with
• Index
• Python Module Index

Indices and tables

• Index

• Python Module Index