This is a package to reproduce the publication on Lobster automation: J. George, G. Petretto, A. Naik, M. Esters, A. J. Jackson, R. Nelson, R. Dronskowski, G.-M. Rignanese, G. Hautier, ChemPlusChem, https://doi.org/10.1002/cplu.202200123
Start_Scripts
includes two scripts to start all Lobster computations with
pymatgen, fireworks, and atomate.
You need to download the data from our second zenodo.org repository first. You can get the data here: https://doi.org/10.5281/zenodo.6373369
wget https://zenodo.org/record/6373369/files/Results.zip?download=1
Please unzip the data and put it in the folder "LobsterAutomation".
You can then use the "Analysis_Scripts" to reproduce our publication.
analyse_results_14_1_11_without_Yb5d.py
will produce the automatic analysis for Yb14Mn1Sb11 with a basis set that does not include 5d (as in the manuscript, aka "small basis").analyse_results_14_1_11__without_Yb5d_anion_anion.py
will produce the automatic analysis including all bonds for Yb14Mn1Sb11 with a basis set that does not include 5d (as in the manuscript, aka "small basis")analyse_results_14_1_11_with_Yb5d.py
will produce the automatic analysis for Yb14Mn1Sb11 with a basis set that does include 5d (as shown in SI, aka "large basis").analyse_results_14_1_11__with_Yb5d_anion_anion.py
will produce the automatic analysis including all bonds for Yb14Mn1Sb11 with a basis set that does include 5d (as shown in SI, aka "large basis")analyse_14_1_11_chemenv.py
will produce the geometric analysis of coordination environments with ChemEnvanalyze_reslts_14_1_11_DOS_Mn.py
will compare the DOS for Mn with the two different basis setsanalyze_reslts_14_1_11_DOS_Sb.py
will compare the DOS for Sb with the two different basis setsanalyze_reslts_14_1_11_DOS_Yb.py
will compare the DOS for Yb with the two different basis setsanalyse_results_GaN.py
will produce all plots and outputs for the GaN phasesanalyse_results_NaCl.py
will produce all plots and outputs for the NaCl phasesanalyse_oxynitrides.py
will produce all plots and outputs for the oxynitride systems
In Analysis_Scripts/Output
, you can find the outputs.
To produce the data, you can use the scripts in "Start_Scripts".
start_workflows_bulk.py
will start all computations except for the oxynitride computationsstart_defect_structures.py
will start the oxynitride computations
The following version numbers are needed for the workflows:
- pymatgen 2022.2.1
- atomate 1.0.3
- enumlib 2.0.4 (Installation with conda)
To analyze the results, you would need Lobsterpy 0.2.1 (which is compatible only with a later version of pymatgen)
The reported computing times are for Intel Xeon E7-4820 v4
CPU type (128 GB RAM per node). We are reporting here the computing times for all the compounds with ISPIN=2
presented in the paper (for the sake of brevity we have excluded oxynitrides and calculations with ISPIN=1
). Objective is just to provide an general overview of time required for performing the calculations and not to account here all the computing times of our calculations.
Material ID | Structure type | Calc Type | Computing time (secs) | NCORES | NODES |
---|---|---|---|---|---|
mp-22851 | NaCl | VASP | 704.975 | 80 | 2 |
lobster | 38 | 40 | 1 | ||
mp-22862 | CsCl | VASP | 798.869 | 80 | 2 |
lobster | 30 | 40 | 1 |
Material ID | Structure type | Calc Type | Computing time (secs) | NCORES | NODES |
---|---|---|---|---|---|
mp-804 | Wurtzite | VASP | 2568.488 | 80 | 2 |
lobster | 265 | 40 | 1 | ||
mp-830 | Zinc-blende | VASP | 2646.004 | 80 | 2 |
lobster | 211 | 40 | 1 | ||
mp-1007824 | BN | VASP | 2491.302 | 80 | 2 |
lobster | 200 | 40 | 1 | ||
mp-2853 | NaCl | VASP | 2494.205 | 80 | 2 |
lobster | 165 | 40 | 1 |
Material ID | Structure type | Calc Type | Computing time (secs) | NCORES | NODES |
---|---|---|---|---|---|
mp-568088 | -- | VASP | 19729.590 | 80 | 2 |
lobsterbasis_0 | 10,215 | 40 | 1 | ||
lobsterbasis_1 | 92,898 | 40 | 1 |