Differences

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--- soft:siman [2023/04/09 16:07] – [Geometrical] a.boev
+++ soft:siman [2023/06/16 17:20] – a.boev
@@ Line 10: / Line 10: @@
 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]]
@@ Line 29: / Line 31: @@
 ==== 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 ====
-  - 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 ====
-  - 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 ====
-  - 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]]