Commit 75f2fbb1 authored by Michele Compostella's avatar Michele Compostella
Browse files

Update README.md

parent badd4c1b
......@@ -79,6 +79,7 @@ exit
```
and examine the output in the $HOME/faved_output/ folder.
For a complete list of Docker commands and options, please check the [Docker documentation](https://docs.docker.com/) and the list of [Docker base commands](https://docs.docker.com/engine/reference/commandline/docker/).
Note that running the Docker container requires root priviledges on the machine. Since, for security reason, Docker is usually not available on computer clusters, it is advisable to use online tools to convert the Docker container into other containerized environment (e.g. Singularity, Linux containers, etc.) in order to run on HPC systems.
......@@ -111,10 +112,10 @@ Once the software run on the Fe sample dataset, the next step is to use the pipe
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:
    bcc_vector.dat
    interstitial_vector.dat
    typea_vector.dat
    vacancy_vector.dat
    bcc_vector.dat
    interstitial_vector.dat
    typea_vector.dat
    vacancy_vector.dat
* 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 named parameters.txt for the FaVaD.py 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 file itself.
* [OPTIONAL] The visualization script for VisIt (vis.py) should be updated with new values for the threshold that controls the number of plotted atoms.
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