pPES

Script to generate and launch PPES calculations with VASP and Quantum Espresso

Installation

Download and setup

First, clone the repository into your local machine:

git clone https://github.com/Enry99/ppes.git

Once the download is completed, go inside the downloaded folder and run:

bash install.sh

to add the executable in the PATH variable. With this operation, you can launch the program from any folder.

Dependencies

The program requires the following Python libraries:

The installation of the dependencies can be done for example with pip, using the command:

python3 -m pip install -r requirements.txt

Program use

To generate the PPES structures, use the command:

ppes gen

To plot the PPES profile, use the command:

ppes plot

All the settings must be provided in a settings.json file (an example with all possible flags is provided inside this repository)

Settings parameters

PPES settings:

range_sweep: range of translation [dz_min, dz_max]. The upper structure will be moved between [z_initial + dz_min, z_initial+dz_max]. The values can be negative.
step: step for the translations
which_coord: coordinate along which the translation is performed (default 'z'). It can be also 'x' or 'y'. All the variables referred to 'upper' belong to the part of the structure which is moved, while 'lower' belong to the part that stays still.
reference_distance: initial distance associated with no translation (dz=0). The distance is calculated according to the corresponding flags, if specified, otherwise it it simply the difference between min(upper) and max(lower)

Input structure(s):
You can either provide a single file containing the upper and lower part using filename_full, specifying the flags for the selection of the upper part, or provide two separate files (filename_upper and filename_lower) with upper and lower structures.

filename_full: path of the file with the full structure (must be in a ASE-readable format)
filename_upper: path of the file with the upper structure (must be in a ASE-readable format)
filename_lower: path of the file with the lower structure (must be in a ASE-readable format)
upper_atoms: selection of atom indices for the "upper" structure, i.e. the one that is moved
upper_species: select the "upper" structure by species
upper_min: select the "upper" structure by the minimum coordinate (e.g. all the atoms with z>zmin if which_coord is 'z')

Distance calculation:
The following settings are used to select the atoms belonging to upper and to lower to calculate the distance. If specified, the distance will be calculated as mean(z_[upper subset]) - mean(z_[lower subset]). If not present, it will simply be min(z_upper) - max(z_lower) These options can be used in conjunction, as the subsetting is done by applying in this order the conditions.

upper_range_fordistance: range [z_min, z_max] to select the upper atoms to average in order to calculate the distance
upper_species_fordistance: species of the upper slab to average in order to calculate the distance
upper_thickness_fordistance: window [min(z_upper), min(z_upper) + upper_thickness_fordistance] to select the upper atoms in order to calculate the distance
lower_range_fordistance: range [z_min, z_max] to select the lower atoms to average in order to calculate the distance
lower_species_fordistance: species of the lower slab to average in order to calculate the distance
lower_thickness_fordistance: window [max(z_lower) - lower_thickness_fordistance, max(z_lower)] to select the lower atoms in order to calculate the distance

DFT program settings:

program: "qe" or "vasp"

For QE:

pwi_head: path for initial part of a pwi file, containing the settings for the calculations (system, electrons, kpoints, etc...)

For VASP:

vasp_pp_path: the directory must contain a folder named 'potpaw_PBE' with all the folders with the name of the elements, each containing its POTCAR
vasp_pseudo_setups: version of the potentials, as a dictionary, e.g. {"base": "recommended", "Li": "_sv"}
poscar_only: write only the POSCAR. The INCAR, POTCAR AND KPOINTS must be present in the current folder
keep_order: keep the order of atoms when writing the output file (this is valid also for QE). Defaults to true when poscar_only is true, otherwise to false

Job submission settings:

launch_sweep: if false, generate only the input file without submitting the sweep (PPES) calculations.
launch_isolated: if false, generate only the files without submitting the calculations for the two isolated structures (upper and lower). Note that if the two structures are provided as a file that contains the energy, e.g. OUTCAR. The calculation is not re-done and that value is used.
jobscript_file. Path of a working jobscript file. For QE you need to include -input $1 >> $2 in the line where pw.x is run.