Packages include functions, objects, etc. that are not natively included in python.
In the course of this practical we will use a number of packages i.e. `ase` for the actual simulation, `numpy` for matrix calculations, `scipy` for curve fitting. To use functions and objects we need to import them:
`import <insert_package_name_here> as <name_of_alias>`
e.g `import numpy as np`
if we want to use just one particular function we can use:
In the course of this practical we will use a number of packages i.e. `ase` for the actual simulation, `numpy` for matrix calculations. To use functions and objects we need to import them, this is done in the scripts.
## Setting up the environment
Before any of the scripts will run, make sure to initialize a virtual environment with all the required packages.
To do this open the directory of this code in a terminal. If you cloned it to your home directory you should acces it via:
`cd <name of clone dir>`
`cd <name of dir you cloned to>`
Then set up the environment here (this one sets up an environment called env).
`python -m venv env`
Now activate the environment:
`source env/bin/activate`
After this your command line should look like thise`(env) <yourusername>@<nameofyourmachine>:/`
After this your command line should look like this `(env) <yourusername>@<nameofyourmachine>:/`
To now include all the packages for the python scripts run:
To work with this code make sure to clone this exact git repo:
`git clone <url of repo>`
## Using Python Packages
Packages include functions, objects, etc. that are not natively included in python.
In the course of this practical we will use a number of packages i.e. `ase` for the actual simulation, `numpy` for matrix calculations, `scipy` for curve fitting. To use functions and objects we need to import them:
`import <insert_package_name_here> as <name_of_alias>`
e.g `import numpy as np`
if we want to use just one particular function we can use:
Before any of the scripts will run, make sure to initialize a virtual environment with all the required packages.
To do this open the directory of this code in a terminal. If you cloned it to your home directory you should acces it via:
`cd <name of clone dir>`
Then set up the environment here (this one sets up an environment called env).
`python -m venv env`
Now activate the environment:
`source env/bin/activate`
After this your command line should look like thise `(env) <yourusername>@<nameofyourmachine>:/`
To now include all the packages for the python scripts run:
`pip install -r requirements.txt`
## Running the code for determining the lattice constants
Run the script:
`python3 minimize_energy_script.py`
The script will ask you to provide initial guesses for the lattice constants and will calculate 300 data points in a range of -0.3 Angstrom and +0.3 Angstrom of your initial guess.
The strain energydentsity csv files are written to the folder `data_min_energy/`
Plot the data and find the minima.
## Running the code for calculating the elastic constants
Run:
`python3 elastic_constants_script.py`
The script will ask you to provide a lattice constant (for the fcc system), a highest and lowest strain (also negative strain i.e. compression) and how many datapoints you would like to evaluate.
The data is written to `data_elastic_constants`. Plot the data and fit a 2nd order polynomial to calccalcualte the elastic constants.
