Commit 9ce3fd91 authored by Michele Compostella's avatar Michele Compostella
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Update with information about using different input files.

parent 11625c0d
......@@ -103,3 +103,24 @@ python3 -p ./parameters.txt
Note however that you are required to change the paths in the parameter.txt file to match the current location of the files and software executables.
## Analyzing new crystal structures
Once the software run on the Fe sample dataset, the next step is to use the pipeline presented here for fingerprinting and visualizing defects in other crystal structures.
In order to do this, the following changes to the pipeline are required:
* An input file for the new structure should be created (e.g. using MD simulations) and stored in the xyz format.
* Files containing the reference descriptor vectors for the undamaged crystal should be provided. In the sample dataset, we supply for this purpose the following four files:
* A text file containing the parameters for the KDTREE code is required (void_code_input.txt in the sample dataset) in order to choose the correct settings for the code.
* The parameter file 'parameters.txt' for the script should be updated with the new locations and names of all the input files. A short description of every keyword is available as comment in the parameter.txt file.
* [OPTIONAL] The visualization script for VisIt ( should be updated with new values for the threshold that controls the number of plotted atoms.
In order to make the new input files available inside the Docker container, the flag
--volume $HOME/new_inputs/:/home/favad/new_inputs/:ro
should be added to the 'docker run' command above. This will mount in read-only mode the '$HOME/new_inputs/' folder and its content from the local machine to the Docker container at the '/home/favad/new_inputs/' location.
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