Minor tweaks to link the doped CCD tutorial where relevant.

docs/src/usage.md

@@ -7,6 +7,9 @@ A typical usage will consist of about three steps; 1. preparation, 2. building `
 Before `CarrierCapture`, you need to calculate potential energy surfaces of atomic vibrations (one-dimensional Configuration Coordinate diagram; `1D-CC`) and _e-ph_ coupling matrix element (`W_if`). Prepare a sequence of structures with displacements which interpolate between two defect states. Run single-point energy calculations on these structures, and extract the total energies. Scripts for preprocessing can be found in `/script` which require the [`pymatgen`](http://pymatgen.org) python library.
 
 1. **Generate `1D-CC`**
+The [`doped`](https://doped.readthedocs.io) Python package provides a tutorial for ensuring appropriately oriented and 
+ordered structures for configuration-coordinate diagram (and NEB path) generation, to ensure appropriate structure 
+interpolation. See the `doped` [NEB/CCD generation tutorial](https://doped.readthedocs.io/en/latest/CCD_NEB_tutorial.html) for this.
 
    1. Calculate equilibrium geometries and total energies of defective supercells with charge states `q`(initial) and `q±1`(final) denoted `Conf.(q)` and `Conf.(q±1)`, respectively.
 

example/notebook/CarrierCapture_workflow.ipynb

@@ -110,7 +110,7 @@
    "id": "869aff64",
    "metadata": {},
    "source": [
-    "- The datapoints (i.e. deformed structures) are generated by a linear interpolation between equilibrium configurations of excited (initial) and ground (final) states, which can be obtained by [gen_cc_struct.py](https://github.com/WMD-group/CarrierCapture.jl/blob/master/script/gen_cc_struct.py), or using the convenience functions in [`doped.utils.configurations`](https://doped.readthedocs.io/en/latest/doped.utils.html#module-doped.utils.configurations). It is important for these structures to have matching orientations/positions (such that they correspond to the shortest linear path between them; i.e. having the defect located in the same position in the supercells and similarly oriented) -- this is automatically ensured using the `doped` functions.\n",
+    "- The datapoints (i.e. deformed structures) are generated by a linear interpolation between equilibrium configurations of excited (initial) and ground (final) states, which can be obtained by [gen_cc_struct.py](https://github.com/WMD-group/CarrierCapture.jl/blob/master/script/gen_cc_struct.py), or using the convenience functions in [`doped.utils.configurations`](https://doped.readthedocs.io/en/latest/doped.utils.html#module-doped.utils.configurations). It is important for these structures to have matching orientations/positions (such that they correspond to the shortest linear path between them; i.e. having the defect located in the same position in the supercells and similarly oriented) -- this is automatically ensured using the `doped` functions, see the discussion in the `doped` [NEB/CCD generation tutorial](https://doped.readthedocs.io/en/latest/CCD_NEB_tutorial.html).\n",
     "\n",
     "- The PES is plotted as a function of one-dimensional (1D) generalised configuration coordinate *Q*, which can be obtained by [get_del_Q.py](https://github.com/WMD-group/CarrierCapture.jl/blob/master/script/get_del_Q.py), or again through python using the convenience functions in [`doped.utils.configurations`](https://doped.readthedocs.io/en/latest/doped.utils.html#module-doped.utils.configurations). $\\Delta Q$ is a collective variable of the mass-weighted deformation $\\Delta Q =\\sum m \\Delta R$.\n",
     "\n",