Part C.1: Preparing Selected Adsorbed Systems For VASP Optimisation¶
After you have selected the binding sites to adsorb adsorbates onto and have placed their associated xyz files into Part_C_Selected_Systems_with_Adsorbed_Species_to_Convert_into_VASP_files (with the desired orientations/rotations), we can proceed to preparing the VASP files for these systems with adsorbates. To do this, set the Step_to_Perform variable in the Run_Adsorber.py script to 'Part C':
Step_to_Perform = 'Part C'
As mentioned previously in Part A: How to optimise your system initially, You also need to create a folder called VASP_Files that contains the following files and folders:
INCAR: This is a VASP file that contains all the information required to run the VASP job (https://www.vasp.at/wiki/index.php/INCAR and https://cms.mpi.univie.ac.at/vasp/vasp/INCAR_File.html).KPOINTS: The KPOINTS file is used to specify the Bloch vectors (k-points) that will be used to sample the Brillouin zone in your calculation (https://www.vasp.at/wiki/index.php/KPOINTS).POTCARs: This is a folder that contains all of thePOTCARfiles for all of the different elements in your models. Each of thePOTCARfiles in this folder need to be labelled asPOTCAR_XX, whereXXis the symbol for the particular element. For example, for the POTCAR to describe Cu, you want to name the POTCAR asPOTCAR_Cu, the POTCAR for C should be calledPOTCAR_C, the POTCAR for H should be calledPOTCAR_H, ….
You want to also include any other files that will be needed. For example, if you are running VASP with the BEEF functional, you need to include the vdw_kernel.bindat file in the VASP_Files folder. An example of VASP_Files folders can be found in Adsorber Examples on Github.
You also want to make sure that your Run_Adsorber.py script also includes the slurm_information dictionary that contains the information required to make the submit.sl file. The submit.sl file is used to submit a VASP job to Slurm. The information required in the slurm_information dictionary can be found at Information required to make submit.sl siles for submitting files to Slurm.
Once you have done all of these requirements, you can then run the Run_Adsorber.py script in the terminal:
python Run_Adsorber.py
What will Run_Adsorber.py: Part C do?¶
Run_Adsorber.py will take all the .xyz that you have placed in Part_C_Selected_Systems_with_Adsorbed_Species_to_Convert_into_VASP_files and convert them into files ready to be run in VASP with the Slurm Workload Manager.
Adsorber will create a new folder called Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP that contain VASP folders of your selected systems with adsorbates. Each of these VASP folders contain a POSCAR of the system with adsorbate, as well as the INCAR, KPOINTS, POTCAR, and submit.sl files, as well as any other files that you need for your VASP calcuations.
If the VASP folder exists and it contains a POSCAR, this POSCAR will not be replaced as you may have updated the POSCAR if your VASP job entered prematurally without converging. If you do want to force override all POSCAR files, you will want to set part_c_force_create_original_POSCAR = True in your Run_Adsorber.py script.
Note: This Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP folder may get big, so just check the amount of space that the newly created Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP is taking up as it is being created.
I accidentally gave wrong settings in the INCAR or submit.sl files, or something about my KPOINTS or POTCAR. What should I do?¶
If you realise you have entered in wrong settings in the INCAR or submit.sl files, or your KPOINTS or POTCAR files are wrong, no problem! Make the changes to these files and then rerun your Run_Adsorber.py script again. Only those jobs that have not begun to run (i.e. dont have an OUTCAR) will have their VASP files INCAR, submit,sl, KPOINTS, POTCAR, and other vast files (not the POSCAR though) copied over. Adsorber will not touch those jobs that have an OUTCAR that are assumed to be running/have finished running.
I want to add more new places that adsorbates can bind to on the surface of the cluster/surface model in Part B, what do I do here?¶
Run your Run_Adsorber.py script once you have included all the new binding sites to your Part_C_Selected_Systems_with_Adsorbed_Species_to_Convert_into_VASP_files folder. Running your your Run_Adsorber.py script again will add new folders and VASP files of these new arrangements of adsorbates on the surface of your cluster/surface model in your Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP folder. Your original POSCAR will not be changed (unless you have set part_c_force_create_original_POSCAR = True. We recommend you not to do this here). Only those jobs that have not begun to run (i.e. dont have an OUTCAR) will have their VASP files INCAR, submit,sl, KPOINTS, POTCAR, and other vast files (not the POSCAR though) copied over. Adsorber will not touch those jobs that have an OUTCAR that are assumed to be running/have finished running.
How to submit VASP jobs to Slurm: The Run_Adsorber_submitSL_slurm.py program¶
Once you have run the Run_Adsorber.py script with Step_to_Perform = 'Part C', you can submit your jobs. If you use a computer cluster that run the Slurm Workload Manager, you can submit all your jobs at the same time by changing directory into the Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP folder and running a script called Run_Adsorber_submitSL_slurm.py.
cd Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP
Run_Adsorber_submitSL_slurm.py
Running the Run_Adsorber_submitSL_slurm.py script in the terminal will submit all your VASP jobs. The Run_Adsorber_submitSL_slurm.py program works by looking through all subdirectories that this program is executed from and looks for folders that contain a 'submit.sl' file.
This program will not submit VASP jobs that are currently running or have been run. This program will only submit VASP jobs that do not contain a ``OUTCAR`` file. Any job that is running or has already run will contain an
OUTCARfile, which tellsRun_Adsorber_submitSL_slurm.pythat that VASP job is currently running or has already been run.Run_Adsorber_submitSL_slurm.pywill execute all folders that contain a'submit.sl'file. However,Run_Adsorber_submitSL_slurm.pywill not run any'submit.sl'files from previously run calculations, which are found in theSubmission_Folderfolders.
If you dont want to run all the jobs in Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP but just a select few, you want to move into that folder and then type Run_Adsorber_submitSL_slurm.py into the terminal. For example, lets say that I only want to run the jobs that are in the directory Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP/COOH_symmetric/Bridge_Sites/Other_5_fold_Sites_Blue, then we want to move into this directory and then type Run_Adsorber_submitSL_slurm.py into the terminal:
cd Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP/COOH_symmetric/Bridge_Sites/Other_5_fold_Sites_Blue
Run_Adsorber_submitSL_slurm.py
Run_Adsorber_submitSL_slurm.py is set up to only allow 1000 jobs to be running or in the queue in slurm. You can change this value in the Run_Adsorber_submitSL_slurm.py, however by default slurm usually only allows for 1000 jobs to be running or in the queue at any one time. Before you run Run_Adsorber_submitSL_slurm.py you can see how many jobs you are submitting to the queue by running typing no_of_submitSL_files into the terminal in the directory you are in. To use this command, you need to include the alias in your ~/.bashrc:
alias no_of_submitSL_files='find . -name "submit.sl" -type f -not -path "*Submission_Folder_*" | wc -l'
For example, if I want to find out all the jobs in Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP, I move into this directory and type no_of_submitSL_files into the terminal:
cd Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP
no_of_submitSL_files
If I want to find out all the jobs in Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP/COOH_symmetric/Bridge_Sites/Other_5_fold_Sites_Blue, I move into this directory and type no_of_submitSL_files into the terminal:
cd Part_C_Selected_Systems_with_Adsorbed_Species_to_Run_in_VASP/COOH_symmetric/Bridge_Sites/Other_5_fold_Sites_Blue
no_of_submitSL_files
To find out the number of jobs that are running or are waiting in the queue in slurm, you can type no_of_jobs_running_or_queued into the terminal. To use this command, you need to enter this alias into your ~/.bashrc:
alias no_of_jobs_running_or_queued='squeue -u $USER | wc -l'
Note: This will give you the number of jobs you have in your slurm queue, plus 1. So whatever number you get from no_of_jobs_running_or_queued, minus 1 from it to get the actual number of jobs in your queue. Not suer how to fix this yet.
NOTE: You CAN enter more than 1000 jobs into the slurm queue with Run_Adsorber_submitSL_slurm.py. If you reach 1000 jobs queued in slurm, Run_Adsorber_submitSL_slurm.py will patiently wait for current running jobs to complete and add more of your jobs into the slurm queue as current jobs are completed.
What to do if some jobs need to be resubmit for some reason¶
If you would like to resubmit one or many jobs for some particualy reason, see Part C.2: What To Do If Some Jobs Have Not Finished/Converged for information about the programs for doing this.