Untitled

This tutorial will guide you through the process of running a single-point and geometry optimization DFT calculations using VASP software. VASP v6.4.3 is pre-installed on CCR and the folder is located in /projects/academic/kaihangs/share/software/vasp including the licensed pseudo potential files. Let’s get started!

Single-Point DFT Calculation

In this section, we are going to perform a single-point DFT calculation on a Mg-MOF-74 system with a CO2 molecule inside the structure. Single-point calculation is basically to perform a DFT calculation of the energy and atomic forces of the system as is. The calculation will be performed using the rev-vdw-DF2 functionals. Planewave basis set with energy cutoff of 520 eV will be used.

First copy the example files to your own CCR folder. For example, under your CCR project space, e.g., /projects/academic/kaihangs/kaihangs , create a test folder and copy the files:
```
mkdir vasp_test
cd vasp_test
cp -r /projects/academic/kaihangs/share/software/vasp/example/Single_point .
cd Single_point
```
Inside the folder, there are files:
- INCAR (input parameters for the run)
- POSCAR (positions of the atoms)
- KPOINTS (k-points used in the calculation)
- run_vasp.job (slurm job script file)
- vdw_kernel.bindat (proprietary pre-calculated vdw kernels)
You can visualize the system, i.e., POSCAR file, using OVITO software by simply dragging the file into the OVITO window:

We are still missing POTCAR file which is the pseudopotentials for the atoms. This file is proprietary. We have purchased the license, and you can create this file by concatenating pseudopotential files for each involving elements. For instance, in the header of the POSCAR file, it says Mg H C O C O , so we need the add ALL pseudopotential files to POTCAR file match the exact same sequence as Mg H C O C O (although C and O appear twice, we still need to add pseudopotentials for C and O twice to match the order). All pseudopotential files are available in /projects/academic/kaihangs/share/software/vasp . In this case, we will use PBE functionals.
```
cd /projects/academic/kaihangs/share/software/vasp/potpaw_PBE.64/
cat Mg/POTCAR H/POTCAR C/POTCAR O/POTCAR C/POTCAR O/POTCAR > your_project_space/Single_point/POTCAR
```
When you publish your paper with VASP simulation input files, you can only publish INCAR, POSCAR and KPOINTS files. vdw_kernel and POTCAR files are proprietary.
With all files ready, you can submit the VASP job through
```
sbatch run_vasp.job
```
You can check the job status:
```
squeue -M all -u **your_CCR_username**
```
<aside> ⚠️ To cancel your job before it finishes, use command scancel -M all <jobid> This is because Slurm commands default to the UB-HPC cluster. You have to specify the faculty cluster (use either the -M faculty or --clusters=faculty option) or all clusters (use -M all). Source: CCR website.

</aside>

The calculation will take a while to finish. Once it finishes, all output data will be in OUTCAR file. Scrolling down to the end of the OUTCAR file, you will find the zero-temperature energy of this CO2 - MgMOF74 system:

  FREE ENERGIE OF THE ION-ELECTRON SYSTEM (eV)
  ---------------------------------------------------
  free  energy   TOTEN  =      -354.60640889 eV

  energy  without entropy=     -354.60640889  energy(sigma->0) =     -354.60640889

--------------------------------------------------------------------------------------------------------

    POTLOK:  cpu time      2.0261: real time      2.0348

-------------------------------------------------------------------------------------------------------

Geometry Optimization Calculation