Commit 17fe1623 authored by Michele Compostella's avatar Michele Compostella

Adapting file names

parent d1e9a360
......@@ -64,12 +64,12 @@ Finally, shell into the Docker container mounting the created folder:
sudo docker run -t -i --volume $HOME/favad_output/:/home/favad/sample/output/ favad /bin/bash
```
Using the previous command, the ouput files generated inside the Docker container will be available in $HOME/faved_output/ of your local machine. Please note that the content of this folder will be overwritten, if the folder is not empty.
Using the previous command, the ouput files generated inside the Docker container will be available in $HOME/favad_output/ of your local machine. Please note that the content of this folder will be overwritten, if the folder is not empty.
At this point you can run the workflow for fingerprinting and visualizing defects on the sample dataset inside the Docker container:
```shell
cd /home/favad/sample/
python3 FaVaD.py -p /home/favad/sample/parameters.txt
python3 FaVAD.py -p /home/favad/sample/parameters.txt
```
When the rendering is completed, you can log out the Docker container using
......@@ -78,7 +78,7 @@ When the rendering is completed, you can log out the Docker container using
exit
```
and examine the output in the $HOME/faved_output/ folder.
and examine the output in the $HOME/favad_output/ folder.
For a complete list of Docker commands and options, please check the [Docker documentation](https://docs.docker.com/) and the list of [Docker base commands](https://docs.docker.com/engine/reference/commandline/docker/).
By default, only a single image (and its components in the different colour channels) for the input dataset is generated.
......@@ -103,7 +103,7 @@ By running the installer, you are accepting the [GAP license agreement](http://w
If you installed the software stack locally, you can run the workflow for fingerprinting and visualizing defects on the sample dataset using
```shell
cd ./sample
python3 FaVaD.py -p ./parameters.txt
python3 FaVAD.py -p ./parameters.txt
```
Note however that you are required to change the paths in the parameter.txt file to match the current location of the files and software executables.
......@@ -131,4 +131,4 @@ In order to make the new input files available inside the Docker container, the
should be added to the 'docker run' command above. This will mount in read-only mode the '$HOME/new_inputs/' folder and its content from the local machine to the Docker container at the '/home/favad/new_inputs/' location.
In the folder 'sample/input/descriptor_vectors' we provide the python scripts (and the associated output files) used to calculate the descript vectors of different crystal structures.
These files provide a starting point for the analysis of new crystal structures obtained from MD simulations.
\ No newline at end of file
These files provide a starting point for the analysis of new crystal structures obtained from MD simulations.
......@@ -19,7 +19,7 @@
#####################################################################################################
##
## General Notes:
## FaVaD: Fingerprint And VisuAlization of Defects. Version: 1.0
## FaVAD: Fingerprinting And Visualization Analyzer of Defects. Version: 1.0
## This software provides a workflow for fingerprinting and visualizing defects in damaged crystal
## structures. The theoretical background is presented in: paper_ID
##
......
......@@ -19,7 +19,7 @@
#####################################################################################################
##
## General Notes:
## FaVaD: Fingerprint And VisuAlization of Defects. Version: 1.0
## FaVAD: Fingerprinting And Visualization Analyzer of Defects. Version: 1.0
## Python script to generate the set of standard descriptor vectors
## Please modify the code to create the chosen reference descriptor vector of the standard defect
## The geometry of the standard defect is defined in a xyz file
......
......@@ -19,7 +19,7 @@
#####################################################################################################
##
## General Notes:
## FaVaD: Fingerprint And VisuAlization of Defects. Version: 1.0
## FaVAD: Fingerprinting And Visualization Analyzer of Defects. Version: 1.0
## Python script to generate the set of standard descriptor vectors
## Please modify the code to create the chosen reference descriptor vector of the standard defect
## The geometry of the standard defect is defined in a xyz file
......
......@@ -19,7 +19,7 @@
#####################################################################################################
##
## General Notes:
## FaVaD: Fingerprint And VisuAlization of Defects. Version: 1.0
## FaVAD: Fingerprinting And Visualization Analyzer of Defects. Version: 1.0
## Python script to generate the set of standard descriptor vectors
## Please modify the code to create the chosen reference descriptor vector of the standard defect
## The geometry of the standard defect is defined in a xyz file
......
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