Update README.md

README.md

@@ -1,8 +1,6 @@
-# CHIC
-**C**oarse-graining **H**ybrid **I**organic **C**rystals.
-
-![Schematic of decorating and coarse-graining the sodalite (**sod**) net](/bin/images/sod-decoration.png)
+![CHIC logo](/docs/source/logo.svg)
 
+**C**oarse-graining **H**ybrid **I**organic **C**rystals.
 
 ## Getting started
 
@@ -15,16 +13,16 @@ by running:
 from chic import Structure
 
 # read in structure and delete oxygen from the pores.
-zif8 = Structure.from_cif('FAWCEN.cif')
-zif8.remove_species('O')
+struct = Structure.from_cif("ZIF-8-sod.cif")
+struct.remove_sites_by_symbol("O")
 
 # compute neighbour list, find atomic clusters, and coarse-grain. 
-zif8.get_neighbours_crystalnn()
-zif8.find_atomic_clusters()
-zif8.get_coarse_grained_net()
+struct.get_neighbours_crystalnn()
+struct.find_atomic_clusters()
+struct.get_coarse_grained_net()
 
 # export structure as TopoCIF.
-zif8.net_to_cif('ZIF-8-sod-cg.cif', write_bonds=True, name='ZIF-8-cg')
+struct.net_to_cif('ZIF-8-sod-cg.cif', write_bonds=True, name='ZIF-8-cg')
 ```
 
 Head over to the [chic docs](https://tcnicholas.github.io/chic/) to see examples
@@ -33,10 +31,10 @@ and more details!
 ## ToDo list
 
 - [x] Add docs.
-- [ ] Add simple distance cut-off algorithm for neighbour list building.
+- [x] Add simple distance cut-off algorithm for neighbour list building.
 - [ ] Add custom implementation of optimised CrystalNN algorithm.
 - [x] Integrate back-mapping code.
-- [ ] Integrate extraction of local energies from LAMMPS dump format.
+- [x] Integrate extraction of local energies from LAMMPS dump format.
 - [ ] Add registry to Net class for easier future development beyond ZIFs.
 
 ## Authors