add the adsorption energy to the docs

docs/source/nodes.rst

@@ -77,3 +77,9 @@ Each Node is documented in the following section.
 
     PermutationInvariance
         .. autofunction:: mlipx.PermutationInvariance
+
+    RelaxAdsorptionConfigs
+        .. autofunction:: mlipx.RelaxAdsorptionConfigs
+
+    BuildASEslab
+        .. autofunction:: mlipx.BuildASEslab

docs/source/recipes.rst

@@ -13,6 +13,7 @@ The following recipes are currently available within :code:`mlipx`.
    recipes/relax
    recipes/md
    recipes/neb
+   recipes/adsorption
    recipes/phase_diagram
    recipes/pourbaix_diagram
    recipes/vibrational_analysis

docs/source/recipes/adsorption.rst

@@ -0,0 +1,39 @@
+.. _neb:
+
+Adsorption Energies
+===================
+
+This recipe calculates the adsorption energies of a molecule on a surface.
+The following example creates a slab of ``Cu(111)`` and calculates the adsorption energy of ethanol ``(CCO)`` on the surface.
+
+.. code-block:: console
+
+   (.venv) $ mlipx recipes adsorption --models mace_mp,sevennet,orb_v2,mattersim --slab-config '{"crystal": "fcc111", "symbol": "Cu", "size": [3,4,4]}' --smiles CCO --repro
+   (.venv) $ compare --glob "*RelaxAdsorptionConfigs"
+
+
+.. jupyter-execute::
+   :hide-code:
+
+   from mlipx.doc_utils import get_plots
+
+   plots = get_plots("*RelaxAdsorptionConfigs", "../../examples/adsorption/")
+   plots["adsorption_energies"].show()
+
+This test uses the following Nodes together with your provided model in the :term:`models.py` file:
+
+* :term:`RelaxAdsorptionConfigs`
+* :term:`BuildASEslab`
+* :term:`Smiles2Conformers`
+
+
+.. dropdown:: Content of :code:`main.py`
+
+   .. literalinclude:: ../../../examples/adsorption/main.py
+      :language: Python
+
+
+.. dropdown:: Content of :code:`models.py`
+
+   .. literalinclude:: ../../../examples/adsorption/models.py
+      :language: Python

examples/adsorption/main.py

@@ -14,9 +14,6 @@
         ).frames
     )
 
-
-# TODO: datapath
-
 adsorbates = []
 
 with project.group("initialize"):

mlipx/nodes/adsorption.py

@@ -31,7 +31,7 @@ class BuildASEslab(zntrack.Node):
     a : float
         (optional) The lattice constant. If specified, it overrides the experimental
         lattice constant of the element. Must be specified if setting up a crystal
-          structure different from the one found in nature.
+        structure different from the one found in nature.
     c : float
         (optional) Extra HCP lattice constant. If specified, it overrides
           the experimental lattice constant of the element.

mlipx/recipes/adsorption.py.jinja2

@@ -11,8 +11,6 @@ with project.group("initialize"):
     slabs.append(mlipx.BuildASEslab(**{{ slab_config }}).frames)
 {% endif %}
 
-# TODO: datapath
-
 adsorbates = []
 {% if smiles %}
 with project.group("initialize"):