https://github.com/jageo/lobsterautomation

This is a package to reproduce the publication on Lobster automation

https://github.com/jageo/lobsterautomation

Repository

This is a package to reproduce the publication on Lobster automation

https://github.com/JaGeo/LobsterAutomation/blob/main/

# LobsterAutomation
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](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](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 ChemEnv
- `analyze_reslts_14_1_11_DOS_Mn.py` will compare the DOS for Mn with the two different basis sets
- `analyze_reslts_14_1_11_DOS_Sb.py` will compare the DOS for Sb with the two different basis sets
- `analyze_reslts_14_1_11_DOS_Yb.py` will compare the DOS for Yb with the two different basis sets
- `analyse_results_GaN.py` will produce all plots and outputs for the GaN phases
- `analyse_results_NaCl.py` will produce all plots and outputs for the NaCl phases
- `analyse_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 computations
- `start_defect_structures.py` will start the oxynitride computations


The following version numbers are needed for the workflows:
- [pymatgen 2022.2.1](https://pypi.org/project/pymatgen/2022.2.1/)
- [atomate 1.0.3](https://github.com/hackingmaterials/atomate)
- [enumlib 2.0.4](https://github.com/msg-byu/enumlib) (Installation with conda)


To analyze the results, you would need Lobsterpy 0.2.1 (which is compatible only with a later version of pymatgen)
- [LobsterPy](https://github.com/JaGeo/LobsterPy)



# Computing times
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. 


## NaCl
| 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   	

## GaN

| 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   

## Yb14MnSb11

| 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   	

Owner

GitHub Events

Issues and Pull Requests

Last synced: about 1 year ago