Update docs for NEB

README.md

@@ -89,7 +89,7 @@ Current and planned features include:
   - NVE
   - NVT (Langevin(Eijnden/Ciccotti flavour) and Nosé-Hoover (Melchionna flavour))
   - NPT (Nosé-Hoover (Melchiona flavour))
-- [ ] Nudge Elastic Band
+- [x] Nudge Elastic Band
 - [x] Phonons
   - Phonopy
 - [x] Equation of State

docs/source/conf.py

@@ -53,6 +53,7 @@
     "phonopy": ("https://phonopy.github.io/phonopy/", None),
     "codecarbon": ("https://mlco2.github.io/codecarbon/", None),
     "torch": ("https://pytorch.org/docs/stable", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None,)
 }
 
 # Add any paths that contain templates here, relative to this directory.
@@ -224,4 +225,5 @@
     ("py:class", "Calculator"),
     ("py:class", "Context"),
     ("py:class", "Path"),
+    ("py:class", "Figure"),
 ]

docs/source/user_guide/command_line.rst

@@ -31,6 +31,7 @@ This should return something similar to:
       eos          Calculate equation of state.
       geomopt      Perform geometry optimization and save optimized structure...
       md           Run molecular dynamics simulation, and save trajectory and...
+      neb          Run Nudged Elastic Band method.
       phonons      Calculate phonons and save results.
       singlepoint  Perform single point calculations and save to file.
       train        Running training for an MLIP.
@@ -451,6 +452,36 @@ with 101 sampling points for each path segment.
    :align: center
 
 
+Nudged Elastic Band
+-------------------
+
+Run the Nudged Elastic Band method (using the `MACE-MP <https://github.com/ACEsuit/mace-mp>`_ "small" force-field):
+
+.. code-block:: bash
+
+    janus neb --init-struct tests/data/N2.xyz --final-struct tests/data/2N.xyz --minimize
+
+
+This will use ASE's built-in `interpolation <https://wiki.fysik.dtu.dk/ase/ase/neb.html#interpolation>`_
+between the minimized initial and final structures, before applying ASE's ``NEBOptimizer``, an adaptive ODE solver,
+to the NEB.
+
+This will save the energy barrier, delta E of the elementary reaction, and maximum force, to a results file, ``N2-neb-results.dat``,
+in addition to generating a log file, ``N2-neb-log.yml``, and summary of inputs, ``N2-neb-summary.yml``.
+
+If a band has already been generated, such as by adding the ``--write-images`` option to the above command,
+this can be passed instead of the initial and final structures:
+
+.. code-block:: bash
+
+    janus neb  --band-structs tests/data/N2-neb-images.xyz
+
+
+Additional options include using `pymatgen to interpolate <https://pymatgen.org/pymatgen.core.html#pymatgen.core.structure.IStructure.interpolate>`_,
+with the ``--interpolator`` option, using `DyNEB <https://wiki.fysik.dtu.dk/ase/ase/neb.html#ase.mep.dyneb.DyNEB>`_ for scaled and dynamic
+optimizations of images through the ``--neb-method`` option, and changing the optimizer using the ``--neb-optimizer`` option.
+
+
 Training and fine-tuning MLIPs
 ------------------------------