Installation¶

Conda¶

The installation procedure is quite simple if you use, highly recommended conda package manager:

conda install -c conda-forge elastic

The above command installs elastic with all dependencies into your current conda environment. If you want to add my anaconda.org channel into your conda installation you need to run following command:

conda config --add channels conda-forge

The above method has additional benefit of providing current installation of ASE and spglib libraries.

PyPi¶

The package is published simultaneously on conda and pypi. The second recommended way to install elastic is with pip:

pip install elastic

which should install the package and all its dependencies. Note that the number of dependencies is rather large and some of them are fairly large. Most of them, however, are just standard scientific python packages - almost all are present in standard anaconda install.

Manual¶

To install the code pedestrian way you need to install following python packages (most, if not all, are available in major linux distributions):

SciPy and NumPy libraries
matplotlib (not strictly required, but needed for testing and plotting)
ASE system
spglib space group library
Some ASE calculator (VASP, GPAW, abinit, …), but be warned that for now the code was developed using VASP only. I will be happy to help you extending it to other calculators. The code can be used without supported ASE calculator using command line interface and external, independent calculation tool.

This is highly system-dependent and I am unable to provide detailed support for this type of install - I use conda install of ASE/elastic myself!

Some legacy installation guides which may help you with manual process could be find at the QE-doc project pages.

Essentially, you need to clone the repository and run:

python setup.py install

in the main directory. But this is really not recommended way to install. Use it at your own risk and if you know what you are doing.

Testing¶

The simplest verification if everything works is just using the elastic utility to see the help screen:

elastic --help

or version of the package:

elastic --version

Additionally the whole package has a set of unittests based on hypothesis package. The tests are self-contained and do not require any external packages like DFT programs (e.g. VASP). You can run these tests by executing following command in the source directory:

python -m unittest discover -s test -b

Usage¶

Starting from ver. 5.0, the command line utility elastic is a primary interface to the package and the direct python programming with the library is relegated to non-standard calculations. The basic calculation scheme can be summarized with the following list:

Prepare the basic structure data in the form of VASP POSCAR file or abinit input file. Support for other programs can be added relatively easily. Contact the author if you need it. The structure should be fully optimized represent what you consider to be ground state of the system.
run elastic on the structure to generate deformed structures probing the properties of the system:
```
elastic -v --cij gen -n 5 -s 2 POSCAR
```
which generates a set of deformed systems named cij_XXX.POSCAR, where XXX is replaced by numbers with 000 corresponding to undisturbed structure.
run your DFT program (VASP, abinit, etc.) on all systems. This step depends on your particular system, and you need to handle it yourself. You need to make sure that for each system the internal degrees of freedom are optimized and full stress tensor gets calculated. Example bash script handling this task on my cluster looks like this:
```
#!/bin/bash

# Command to run vasp in current directory
RUN_VASP="/opt/bin/run-vasp541"

for s in $* ; do
    d=${s%%.POSCAR}
    echo -n  $d ": "
    mkdir calc-$d
    (
        cd calc-$d
        ln -s ../INCAR ../KPOINTS ../POTCAR ../vasprun.conf .
        ln -s ../$s POSCAR
        $RUN_VASP
    )
done
```
This produces a set of directories: calc-cij_XXX with completed single-point calculations.
run elastic again to post-process the calculations. We do that by feeding it with output from the DFT calculations. Remember to put undisturbed structure at the first position:
```
elastic -v --cij proc calc-cij_000/vasprun.xml calc-cij_*/vasprun.xml
```

You can test this procedure using data provided as a reference in the tests/data directory. If you run the script on the provided data you should get following output:

elastic -v --cij proc calc-cij_000/vasprun.xml calc-cij_*/vasprun.xml

Cij solution
------------------------------
 Solution rank:  3
 Square of residuals: 0.00053
 Relative singular values:
 1.0000   0.7071   0.6354

Elastic tensor (GPa):
   C_11     C_12     C_44
------------------------------
 321.15    95.88   143.44

The data provided correspond to cubic MgO crystal. The DFT calculation setup is tuned to provide quick results for testing and should not be used as a guide for production calculations. You need to determine proper calculation setup for your system.