High throughput molecular dynamics workflow for generating atomistic databases of defect transport in chemically complex materials.
The Hop-Decorate code has 2 main functionalities:
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Given an atomic configuration representing some material at the atomic scale with some defect present, Hop-Decorate automatically either runs molecular dynamics on that atomic configuration at a user defined temperature in order to discover defect transitions or conducts a Dimer search [1] for a new transition. The energy barrier of the discovered transition is then calculated with an implementation of the Nudged Elastic Band (NEB) method [2]. This searching and NEB calculation process is completed iteratively to generate a database of possible transitions that the defect can make in the material which can be returned to the user.
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The other functionality requires the code to know about a defect transition from one stable configuration to another, either as an input by the user or discovered by the previously described routine. Regardless of the source of the transition between atomic configurations, the code calculates how the energy barrier of the transition changes when the atoms are assigned to be different atomic species with concentrations provided by the user. For example, the user may input that they are interested in a 50:50 Cu:Ni ratio alloy. The code would then randomly assign atoms in the atomic configurations as Cu or Ni at a ratio of 50:50 and then recompute the energy barrier of the transition of interest. This would generate a distribution of energy barriers and other statistics which are returned to the user.
These two functions are used together in the code to automatically generate transitions between defect configurations and calculate the distribution of energy barriers of a given transition and user defined alloy composition.
[1] Henkelman, Graeme, and Hannes Jónsson. "A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives." The Journal of chemical physics 111.15 (1999): 7010-7022.
[2] Henkelman, Graeme, Blas P. Uberuaga, and Hannes Jónsson. "A climbing image nudged elastic band method for finding saddle points and minimum energy paths." The Journal of chemical physics 113.22 (2000): 9901-9904.
List of third-party python libraries that this code requires to run:
It is recommended that you install these in a conda requirement leverging the requirements.txt file. For example, setting up your conda environment will look something like this:
conda create --name my_env
conda activate my_env
conda install -c conda-forge --file /path/to/requirements.txt This can take some time...
Some users have reported issues with installing ASE with conda, if you also have problems consider using pip:
pip install aseIt is then recommended to add these lines to your .zshrc or .bashrc:
export PATH=$PATH:/path/to/Hop-Decorate/
export PYTHONPATH=$PYTHONPATH:/path/to/Hop-Decorate/ If you encounter any bugs, have feature requests, or want to discuss anything related to the project, feel free to join the Slack channel #Hop-Decorate.
- All structures that you pass to the code need to have [0,0,0] as their origin.
- All structures must also be cubic
This program underwent formal release process with Los Alamos National Lab with reference number O4739
© 2024. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare. derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
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