Update paper.md

GBs are geometrical entities with a large parameter space that has been well formulated within a coincident site lattice (CSL) mathematical framework [@Sutton:1996]. One important computational advantage of the CSL formalism is that it enables the construction of GBs in a periodic setup for atomistic simulations. ``GB_code`` [@GB_code] uses the CSL construction to generate GB atomic structures (currently for cubic materials) systematically. It provides input atomic structures for large-scale atomistic simulations with interatomic potentials (as implemented e.g. in ``LAMMPS`` [@LAMMPS:1995]) or _ab initio_, density-functional-theory (DFT) simulations (as implemented e.g. in ``VASP`` [@VASP:1996]). These atomistic codes can further calculate different properties of the GBs. In addition to providing the input structures, the ``csl_generator.py`` script and the attached Jupyter notebooks have extra functionality to show how the CSL properties can be used to locate, classify and categorize different GBs and to extract detailed information about them.

``GB_code`` is designed to be a command line tool as it is documented in detail in the README file of the repository,

but the modules can also be accessed separately for example via the attached Jupyter notebooks. The code consists of two main scripts, ``csl_generator.py`` and ``gb_generator.py``, that should be used in this order to produce the final GB structures. The attached Jupyter notebooks in the Test directory, ``Usage_of_GB_code.ipynb`` and ``Dichromatic_pattern_CSL.ipynb``, input the two scripts as modules. The former addresses the general usage of the code with some extra tips and functions to locate GBs of interest, the latter depicts how CSL properties such as the overlapping patterns and displacement shift complete (DSC) vectors can be extracted and visualized. In the notebooks, two examples of the usage of the ``GB_code`` in our previous publications [@Pub1:2016, @Pub2:2018] have been shown as well.

but the modules can also be accessed separately for example via the attached Jupyter notebooks. The code consists of two main scripts, ``csl_generator.py`` and ``gb_generator.py``, that should be used in this order to produce the final GB structures. The attached Jupyter notebooks in the Test directory, ``Usage_of_GB_code.ipynb`` and ``Dichromatic_pattern_CSL.ipynb``, input the two scripts as modules. The former addresses the general usage of the code with some extra tips and functions to locate GBs of interest, the latter depicts how CSL properties such as the overlapping patterns and displacement shift complete (DSC) vectors can be extracted and visualized. In the notebooks, two examples of the usage of the ``GB_code`` in our previous publications [@Pub1, @Pub2] have been shown as well.

``GB_code`` uses the analytical and mathematical formulations of the following works of @Sutton:1996, @Bollmann:1982, @Grimmer:1974. Some functionality from the code by @Marcin on CSL has been used in a modified form in the ``GB_code``.