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soft:siman [2023/04/09 10:20] – a.boevsoft:siman [2023/06/16 17:20] – a.boev
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 ====== Siman Wiki ====== ====== 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/ - 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 ===== ===== Tutorials =====
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   - [[https://nbviewer.org/github/dimonaks/siman/blob/master/tutorials/create_vasp_calculation.ipynb| Making VASP calculations including optimization of lattice constants]]   - [[https://nbviewer.org/github/dimonaks/siman/blob/master/tutorials/create_vasp_calculation.ipynb| Making VASP calculations including optimization of lattice constants]]
-  - Create supercells +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/supercells.ipynb|Create supercells]] 
-  - DOS calculation +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/dos.ipynb|DOS calculation]] 
-  - Band structure calculation +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/bands.ipynb|Band structure calculation]] 
-  - Bader charges calculation+  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/bader.ipynb|Bader charges calculation]]
  
 ==== Geometrical ==== ==== Geometrical ====
-  - Point defects +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/geo_point_surf/point_defects.ipynb|Point defects]] 
-  - Surfaces +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/geo_point_surf/surface.ipynb|Surfaces]] 
-  - Build arbitrary surfaces+  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/surfaces.ipynb|Build arbitrary surfaces]]
  
 ==== Advanced calculations ==== ==== Advanced calculations ====
-  - Calculate migration barriers +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/neb.ipynb|Calculate migration barriers]] 
-  - Wrapper for migration barriers (beta) +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/calc_barriers_subroutine.ipynb|Wrapper for migration barriers (beta)]] 
-  - Occupation matrix control +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/OMC.ipynb|Occupation matrix control]] 
-  - Reconstruction of surface with Monte-Carlo method +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/surface_MC.ipynb|Reconstruction of surface with Monte-Carlo method]] 
-  - Migration of small polarons+  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/simanaks/tutorials/polaron.ipynb|Migration of small polarons]]
  
 ==== Specific for Li-ion cathode materials ==== ==== Specific for Li-ion cathode materials ====
-  - Create deintercalated structure +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/deintercalate.ipynb|Create deintercalated structure]] 
-  - Additional control of siman+==== Additional control of Siman====
  
-==== Changing calculation parameters ==== +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/creating_sets.ipynb|Changing calculation parameters]] 
-  - Choosing k-points +  -[[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/kpoints.ipynb| Choosing k-points]] 
-  - Reading xyz files+  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/read_xyz.ipynb|Reading xyz files]]
  
 ==== Drafts ==== ==== Drafts ====
-  - Plotting DOS grids+  - [[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 ==== ==== Currently relevant only for Skoltech users ====
-  - Working with CEE database +  - [[http://nbviewer.jupyter.org/github/dimonaks/siman/blob/master/tutorials/working_with_database.ipynb|Working with CEE database]] 
-  - TODO+  - [[https://github.com/dimonaks/siman/wiki/TODO|TODO]]
  
  
soft/siman.txt · Last modified: 2024/04/16 12:56 by a.boev
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