This is a tiny scripting tool to support annoying preparation of DFT calculations especially in layered materials.

ASE > 3.18.1, numpy, spglib

This program is still constructing status. Please use virtualenv & be careful to install.

git clone https://github.com/eminamitani/layeredMaterialToolKit.git
cd cd layeredMaterialToolKit/
pip install -e .

Normaly, three files are required to setup calculation condition. The name of files are not specified, here I add some explanation on sample files including this repository.

input_data.txt : text file for dictionary of Quantum-espresso calculation

config.txt: text file for dictionary of the other set-ups

PBS_header.txt: text file contains the header section of jobscript.

In the constructor of espresso class, the information of pseudopotetials in target directory is parsed automatically and stored in self.pseudopotentials.

see MoS2-sample for setting the input_data, config, PBS_header etc.

generate_different_lattice_constant_inputs module to create input files to manual optimization for lattice constant. (to avoid trap local minimum in vc-relax) This function creates several directories to run pw.x calculation and store the results. run.sh is also created to submit the job in cluster machines. The headers of job schedulers and mpi commands are specified through PBS_header and config files.

gather_optimize_results module to gather the calculation results in the directories generated by generate_different_lattice_constant_inputs. Used to determine most stable structures & generate scf calculation input with the optimized structure.

create_band_input module to generate band structure input for pw.x & bands.x. See band-test/band_test.py

create_phonon_input module to generate phonon calculation input. To reduce the calculation time, here I assume that phonon calculations are split into several jobs. The number of jobs are determined by njobs in phonon_config. This module generates njobs directories and stores input files for each directory. This module also generates runall.sh script to submit all jobs. See phonon_test/phonon_test.py.

gather_phonon_info module to gather the calculation results stored in several directories generated by create_phonon_input. In order to calculate phonon band structure, this module also generate input files for q2r.x & matdyn.x. The number of q-point in phonon band calculation are given by 'nbandkpts' in phonon_condig. If you set 'calcRun':True in phonon_config file, q2r.x & matdyn.x call directory from this python script. If you set 'wfClean':True , the wavefuntion files are removed to save your storage. See phonon_test/phonon_post.py.

{
'nscfkpts':[24,24,1],
'nphmesh':[6,6,1],
'njobs':4,
'fildvscf':'dvscf',
'tr2_ph':1.0e-16,
'ldisp':True,
'epsil':True,
'trans':True,
'search_sym':False,
'nbandkpts':100,
'wfClean':True,
'calcRun':False,
}