Part D: Supplementary Methods

Often because there are lots of ways that adsorbates can be bound to a cluster, many VASP jobs are required where an adsorbate is bound to various surface sites about a surface or cluster. This means that 200 to 2000+ VASP jobs need to be completed to understand the preferable binding site for an adsorbate upon a surface or cluster. For this reason, I often will perform Adsorber at a low convergence (for example 0.03 eV) and then once I know which sites are most preferable for an adsorbate to bind to, only perform a tigher convergence (0.01 eV) on those lowest energy sites.

Furthermore, in some cases, some of your VASP jobs will converge the adsorbate to the same place on the surface as many other VASP jobs (for example, adsorb a COOH to the same top-top site starting at different positions on your surface). You can use the Part_D_Information_on_VASP_Calculations.xlsx excel spreadsheet to look to see this, by looking at the columns Similar to and No of surface atoms adsorbed to. If either of these are the same as other systems (other rows), this may indicate that those systems (rows) are equivalent.

The following methods can help you figure out if different VASP jobs have converged to the same place and help resume any jobs that you want to tighten the convergence of

Adsorber compare: Comparing systems where adsorbate binds to the same surface atoms

As well as using the Similar to and No of surface atoms adsorbed to columns of the Part_D_Information_on_VASP_Calculations.xlsx excel spreadsheet, you can also use this program to help figure out which systems converged to the same place. This program will look through your Part_D_Information_on_VASP_Calculations.xlsx excel spreadsheet, compare those systems that have the same No of surface atoms adsorbed to, and write files to help you analyse those systems that may be similar.

It is useful to know which system converge to the same place, because if you want to tighten the convergence criteria you don’t need to waste computer time resuming calculations for system that have already converged to the same place with looser convergence criteria. Tightening the convergence of these system may run in identical fashions, therefore only wasting computer time.

To use this program, you want to first move into the same directory as your general.py, adsorbate.py, partA.py, partB.py, and partC.py scripts, and then type Adsorber compare into the terminal:

cd into_the_same_directory_as_your_Run_Adsorber_script
Adsorber compare write_similarity_traj_files upper_energy_limit

You can have the following optional inputs:

  • write_similarity_traj_files (bool): If true, this program will write all the systems that were identical/similar to the same .traj file. This is to allow the user to check that all these systems are infact the same or similar enough to be regarded the same (‘Default: false’).

  • upper_energy_limit (float): By default, all of the lowest energy version of identical final state systems is written to this system. If you only want to write those that are X.XX eV above the minimum energy system, set this value to X.XX eV. For example, if you only want to record those systems that are 0.5 eV above the minimum energy system, set this value to 0.5. (Default: record all lowenergy energy versions of identical states).

This will create a folder called Similar_Systems into your Part_D_Results_Folder directory. This folder will contain subdirectories that are name in the same way as in your Part_D_Information_on_VASP_Calculations.xlsx excel spreadsheet (for example, 1 (C1 [79->25]),1 (O1 [80->66]). However this will be relabelled so that spaces are changed to _, [, ], (, and ) removed, , to + and -> to to, e.g. 1 (C1 [79->25]),1 (O1 [80->66]) goes to 1_C1_79to25__1_O1_80to66). These alternative names are also give in the Part_D_Information_on_VASP_Calculations.xlsx excel spreadsheet, in the cell to the right of this cell. In these folders will contain:

  • similar_systems.txt: This file contains all the job_names, energies, and paths of VASP jobs that may have converged to the same place

  • a traj file: This contains all the final states of your jobs. The images in this traj are ordered in the same manor as given in similar_systems.txt. The images in this traj may all look the same, because these jobs may have converged to the same place.

  • xyz files: These are xyz files of the final states that jobs had reached before finishing. These xyz files may all look the same, because these jobs may have converged to the same place.

What to do once you have performed Adsorber compare and want to tighten the convergence criteria for selected unique states

Once you have performed Adsorber compare, a file called similar_systems.txt will be created. You can run your prepare_unconverged_VASP_jobs.py script again if you want to tighten your convergence critera. In this example, we will call this script prepare_unconverged_VASP_jobs_PartD.py. This is what you need to do in order to tighten the convergence criteria:

  1. Change the EDIFF tag in your INCAR file in your VASP_Files folder to a tighter convergence criteria

  2. You then want to change path_to_resubmission_list_file in your prepare_unconverged_VASP_jobs_PartD.py file to the similar_systems.txt file you have just created. For example, if you want to resubmit those unique states for CHO adsorbates adsorbed to your system, the following code could be used:

Notes about this prepare_unconverged_VASP_jobs_PartD.py script:

  • You can give path_to_resubmission_list_file as a single path or a list of paths.

  • MAKE SURE THAT THE force_prepare VARIABLE IS SET TO True.

  • MAKE SURE THAT THE update_VASP_files VARIABLE IS SET TO True.

prepare_unconverged_VASP_jobs_PartD.py
 1from Adsorber import Run_Adsorber_prepare_unconverged_VASP_jobs
 2
 3# If you want to resubmit certain adsorbate+systems given in a text file. 
 4# There are two ways you can do this, as a single path or a list of paths 
 5# Example 1. Single path
 6path_to_resubmission_list_file = 'Part_D_Results_Folder/Similar_Systems_COH_extra.txt'
 7# Example 1. List of paths
 8path_to_resubmission_list_file = []
 9for system in ['C','CH','CH2','CH3','CH2O','CH2OH','CH3O','CHOH','O','OH']:
10        path_to_resubmission_list_file.append('Part_D_Results_Folder/Similar_Systems_'+str(system)+'.txt')
11
12# A switch that determines what type of resubmnission scheme you would like to perform
13prepare_jobs_switch = 'text' # 'folder' # text
14# Information required to prepare jobs
15main_information = {'path_to_resubmission_list_file': path_to_resubmission_list_file}
16
17# if you would like to prepare jobs even if they have already converged, change this to True
18force_prepare = True # MAKE SURE THIS IS SET TO TRUE
19# If you want to also update the VASP files while performing this task
20update_VASP_files = True # MAKE SURE THIS IS SET TO TRUE
21
22slurm_information = {}
23slurm_information['project'] = 'uoo02568'
24slurm_information['partition'] = 'large'
25slurm_information['time'] = '72:00:00'
26slurm_information['nodes'] = 1
27slurm_information['ntasks_per_node'] = 12
28slurm_information['mem-per-cpu'] = '1200MB'
29slurm_information['email'] = 'geoffreywealslurmnotifications@gmail.com'
30slurm_information['vasp_version'] = 'VASP/5.3.5-intel-2017a-VTST-BEEF'
31slurm_information['vasp_execution'] = 'vasp_cd'
32
33Run_Adsorber_prepare_unconverged_VASP_jobs(prepare_jobs_switch,main_information=main_information,slurm_information=slurm_information,force_prepare=force_prepare,update_VASP_files=update_VASP_files)

  1. Run the prepare_unconverged_VASP_jobs_PartD.py script

python prepare_unconverged_VASP_jobs_PartD.py

This will prepare your unique states to be reoptimised with VASP using a tighter convergence criteria. See Part C1: How to submit VASP jobs to Slurm: Adsorber submit to learn how to submit your VASP jobs to slum.

If you need more information about prepare_unconverged_VASP_jobs.py, see What to do if you want to resubmit jobs to slurm. This prepare_unconverged_VASP_jobs.py script has been written for preparing unconverged jobs for resubmission, but by setting force_prepare = True and update_VASP_files = True we can use this same script for preparing jobs to tighten the convergence criteria.

Adsorber tidy: Clean up the files for jobs that you are happy with

VASP makes lots of files after it has run. These can be annoying to keep if you are transferring files about. The Run_Adsorber_Tidy_Finished_Jobs.py script will get rid of all the unnecessary files that are created from all subdirectories. The files that are removed are: CHG, CHGCAR, CONTCAR, DOSCAR, EIGENVAL, fe.dat, IBZKPT, OSZICAR, PCDAT, POTCAR, REPORT, vasprun.xml, vaspout.eps, WAVECAR, XDATCAR, and vdw_kernel.bindat. The INCAR, KPOINTS, OUTCAR, POSCAR, and submit.sl files are not removed, as well as any output and error files that are created by slurm during the VASP optimsation, are NOT removed by this script. To perform this script, move into the folders that can all the subfolders you wish to tidy up and enter Run_Adsorber_Tidy_Finished_Jobs.py into the terminal:

Adsorber tidy

If you do want to remove all INCAR, KPOINTS, and submit.sl files in these folders as well, move into the folders that can all the subfolders you wish to tidy up and enter Run_Adsorber_Tidy_Finished_Jobs.py full into the terminal:

Adsorber tidy full

Note: the Adsorber tidy command will not change or remove any files that are in your VASP_Files folder.