====== Siman Wiki ======

===== About =====
[[https://github.com/dimonaks/siman|Github page]]

SIMAN documentation, makes DFT calculation easy

[[https://siman.readthedocs.io/en/latest/|Autodoc]]

[[https://pypi.org/project/siman/|How to install with pip]]


[[https://docs.google.com/document/d/1IEY9gLVjEL8gAQrz7lTRFfg-jQbrr5tKZR9XGj_prCE/edit#|Internal siman manual]] 
===== Citation =====
//Aksyonov et. al, Understanding migration barriers for monovalent ion insertion in transition metal oxide and phosphate based cathode materials: A DFT study, [[https://doi.org/10.1016/j.commatsci.2018.07.057|Comp. Mat. Sci. 154, 449-458, 2018]]
//
===== Tutorials =====

==== General ====

  - [[https://nbviewer.org/github/dimonaks/siman/blob/master/tutorials/create_vasp_calculation.ipynb| Making VASP calculations including optimization of lattice constants]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/supercells.ipynb|Create supercells]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/dos.ipynb|DOS calculation]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/bands.ipynb|Band structure calculation]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/bader.ipynb|Bader charges calculation]]

==== Geometrical ====
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/geo_point_surf/point_defects.ipynb|Point defects]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/geo_point_surf/surface.ipynb|Surfaces]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/surfaces.ipynb|Build arbitrary surfaces]]

==== Advanced calculations ====
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/neb.ipynb|Calculate migration barriers]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/calc_barriers_subroutine.ipynb|Wrapper for migration barriers (beta)]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/OMC.ipynb|Occupation matrix control]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/surface_MC.ipynb|Reconstruction of surface with Monte-Carlo method]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/polaron.ipynb|Migration of small polarons]]

==== Specific for Li-ion cathode materials ====
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/deintercalate.ipynb|Create deintercalated structure]]
==== Additional control of Siman====

  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/creating_sets.ipynb|Changing calculation parameters]]
  -[[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/kpoints.ipynb| Choosing k-points]]
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/read_xyz.ipynb|Reading xyz files]]

==== Drafts ====
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/DOS_grid.ipynb|Plotting DOS grids]]
  - [[https://colab.research.google.com/drive/1PbPlZVk-dE6RX9_mvIVxxymOQPF7BeKQ#scrollTo=6dK2HYCKbWWE|Structure() object description]]
  - [[https://colab.research.google.com/drive/1FEC6hc9EeeQyHXqmo2G5MaeEtbGz0QrX|Fitplot]]

==== Currently relevant only for Skoltech users ====
  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/working_with_database.ipynb|Working with CEE database]]
  - [[https://github.com/dimonaks/siman/wiki/TODO|TODO]]


===== File examples =====
Example of {{ :soft:project_sets.py.gz |project_sets.py}}  with sets used for calculation of cathode materials

Example of {{ :soft:interface.zip |interfaces.py}} 

===== For developers =====
  * [[siman:dev:req|Requirements for tests]] 
  * [[siman:dev:des|Description format]]