Add NEB (#393)

* Refactor setting minimize_kwargs

* Add NEB calculation

* Add interpolation options

* Add NEB CLI

* Write NEB results

* Fix reading NEB band

* Fix NEB band structures input

* Fix NEB band structures input

* Fix NEB CLI

* Catch pymatgen error

* Update docs

* Add steps option for NEB

* Fix docstrings

* Update docs for NEB

* Log choice of interpolator

* Rename parameter for wrting band

* Add tests for NEB

* Add NEB CLI command to README

* Use default neb_kwargs

* Tidy setting interpolator and docstrings

* Fix read_kwargs docstrings

Author: ElliottKasoar

README.md

@@ -104,7 +104,7 @@ 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
@@ -210,6 +210,7 @@ janus geomopt
 janus md
 janus phonons
 janus eos
+janus neb
 janus train
 janus descriptors
 janus preprocess

docs/source/apidoc/janus_core.rst

@@ -65,6 +65,17 @@ janus\_core.calculations.md module
    :undoc-members:
    :show-inheritance:
 
+janus\_core.calculations.neb module
+-----------------------------------
+
+.. automodule:: janus_core.calculations.neb
+   :members:
+   :special-members:
+   :private-members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
 janus\_core.calculations.phonons module
 ---------------------------------------
 
@@ -136,6 +147,16 @@ janus\_core.cli.md module
    :undoc-members:
    :show-inheritance:
 
+janus\_core.cli.neb module
+--------------------------
+
+.. automodule:: janus_core.cli.neb
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
 janus\_core.cli.phonons module
 ------------------------------
 

docs/source/conf.py

@@ -54,6 +54,7 @@
     "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.
@@ -225,4 +226,5 @@
     ("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.
@@ -483,6 +484,36 @@ 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
 ------------------------------
 

janus_core/calculations/eos.py

@@ -22,7 +22,7 @@
     PathLike,
 )
 from janus_core.helpers.struct_io import output_structs
-from janus_core.helpers.utils import none_to_dict
+from janus_core.helpers.utils import none_to_dict, set_minimize_logging
 
 
 class EoS(BaseCalculation):
@@ -257,12 +257,9 @@ def __init__(
             raise ValueError("Please attach a calculator to `struct`.")
 
         if self.minimize and self.logger:
-            self.minimize_kwargs["log_kwargs"] = {
-                "filename": self.log_kwargs["filename"],
-                "name": self.logger.name,
-                "filemode": "a",
-            }
-        self.minimize_kwargs["track_carbon"] = self.track_carbon
+            set_minimize_logging(
+                self.logger, self.minimize_kwargs, self.log_kwargs, track_carbon
+            )
 
         # Set output files
         self.write_kwargs.setdefault("filename", None)

janus_core/calculations/md.py

@@ -43,7 +43,7 @@
     PostProcessKwargs,
 )
 from janus_core.helpers.struct_io import input_structs, output_structs
-from janus_core.helpers.utils import none_to_dict, write_table
+from janus_core.helpers.utils import none_to_dict, set_minimize_logging, write_table
 from janus_core.processing.correlator import Correlation
 from janus_core.processing.post_process import compute_rdf, compute_vaf
 
@@ -493,13 +493,9 @@ def __init__(
             self.minimize_kwargs["write_kwargs"] = {"filename": opt_file}
 
         # Use MD logger for geometry optimization
-        if self.logger:
-            self.minimize_kwargs["log_kwargs"] = {
-                "filename": self.log_kwargs["filename"],
-                "name": self.logger.name,
-                "filemode": "a",
-            }
-        self.minimize_kwargs["track_carbon"] = self.track_carbon
+        set_minimize_logging(
+            self.logger, self.minimize_kwargs, self.log_kwargs, track_carbon
+        )
 
         self.dyn: Langevin | VelocityVerlet | ASE_NPT
         self.n_atoms = len(self.struct)