Installation

Clone this repo using the following commands:

cd /path_to_home_directory/
git clone https://github.com/sreeharshab/scalar_codes.git

After successful cloning of the repo, open your .bashrc and insert this line:

export PYTHONPATH=/path_to_home_directory/scalar_codes:$PYTHONPATH

Exit your .bashrc and source it as follows:

source .bashrc

Note: Ensure that you have Atomic Simulation Environment (ASE), Numpy, Pandas, SciPy and Matplotlib installed in your machine!

Optional: scalar_codes can be used as a package if /path_to_home_directory/ is appended to PYTHONPATH.

Resources

There are two parts to this repository. Part 1 is available in pipelines.py and part 2 is available in silicon.py.

Use help() to get detailed documentation about the resources. Furthermore, there are examples for some of the resources in the examples folder.

Note: Presently, documentation is available for all resources in pipelines.py. Full documentation will be available soon.

The defaults for all VASP related calculations are as follows: gga="PE", lreal="Auto", lplane=True, lwave=False, lcharg=False, ncore=8, prec="Normal", encut=300, ediff=1e-6, algo="VeryFast", ismear=-5, gamma=True
You can change the defaults and add additional settings using opt_levels parameter for geo_opt and surface_charging and using addnl_settings parameter for all other calculations.

Part 1: Automation Codes for VASP Related Calculations

1. cell_opt: Optimizes the size of the simulation cell.
2. axis_opt: Optimizes the size of the required axis of the simulation cell.
3. geo_opt: Performs geometry optimization on the system using inbuilt VASP optimizer (IBRION=2) or ASE's BFGS optimizer.
4. bader: Performs bader charge analysis on the system. Charges can be viewed in ACF.dat file or using ase gui and choosing the Initial Charges label in the view tab.
5. COHP: Performs Crystal Orbital Hamilton Population analysis on the system using LOBSTER. Note: Currently, only non spin polarized calculations are supported.
6. frequency: Performs vibrational analysis on the system using VASP or ASE. Use ASE for calculations involving large systems as it supports a parallel scheme.
7. surface_charging: Performs surface charging calculation using VASPsol.
8. gibbs_free_energy: Gives the gibbs free energy of the system. If surface_charging is used, the parabola fit is used to obtain the energy vs potential. If geo_opt is used, OUTCAR is used to obtain energy. The vibrational energy is obtained using the frequency class. These energies can be used in PyEnergyDiagrams to generate reaction pathways.
9. dos: Performs a DOS calculation. Note: The code for visualizing DOS will be implemented soon.
10. analyse_GCBH: Performs a visual analysis of the results from Grand Canonical Basin Hopping simulation performed using catalapp.
11. get_neighbor_list: Provides the neigbor list for the system. Output is provided in Neighbor_List.txt file. Neighbors of each atom, their positions and coordination numbers of each atom are provided based on ASE's natural cutoff distances.
12. check_run_completion: Checks for completion of a VASP job at the provided location.
13. get_cell_info: Provides information about the volume, vector lengths and angles of the unit cell.
14. benchmark: Performs computational benchmark of a VASP job.

Part 2: Codes to Study Silicon Systems

15. create_sigma3_gb: Creates a Σ3 grain boundary with n layers using top_grain.vasp and bottom_grain.vasp files (available in the examples folder).
16. slide_sigma3_gb: Slides Σ3 grain boundary. Serial and parallel runs are implemented. In each run, step and linear schemes are implemented. Note that step scheme is effective for studying the stick-slip sliding behavior and linear scheme is effective for studying elastic deformation.
17. intercalate_Li: Inserts Li in all the interstice positions of Σ3 grain boundary.
18. symmetrize_Si100_surface: Symmetrizes Si (100) strcuture along z axis. This is necessary to perform surface charging calculations using VASPsol.
19. cure_Si_surface_with_H: In order to study Si surfaces, it is essestial to create a bulk like environment far from the surface. To create this environment, we need to add hydrogens to our surface model (with vacuum) to cure the dangling bonds. This code inserts works best for (100) Si surface where it insertes two hydrogens if the coordination of silicon is less than four.