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
- External Programs that will be useful to install for using
Adsorber
- Guide To Using Adsorber
- Prelude 1: Setting your
general.py
andadsorbate.py
scripts - Prelude 2: How to obtain some of the settings for the
adsorber.py
script - Part A: How to optimise your system, as well as optimise adsorbates and other molecules
- Part B1: Adsorbing Adsorbates to your System
- 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 withAdsorber
- How to automate the copying of these
xyz
files: Usingcopy_files_from_folder_B_to_C.py
- What To Do Once You Have Placed Selected
xyz
Files IntoPart_C_Selected_Systems_with_Adsorbed_Species_to_Convert_into_VASP_files
- How to choose which
- Part C1: Preparing Selected Adsorbed Systems For VASP Optimisation
- Part C1: How to submit VASP jobs to Slurm:
Adsorber submit
Adsorber submit
settings that can be changedAdsorber 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
- Part D: Supplementary Methods
- Index
- Python Module Index