Merge pull request #62 from molssi-seamm/dev

Added molecule id for atoms, for LAMMPS
molssi-seamm · Mar 6, 2023 · db7556a · db7556a
2 parents a047442 + ebae439
commit db7556a
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 1 deletion.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,9 @@
 History
 =======
 
+2023.3.5 -- Added molecule numbers for LAMMPS input
+   * Added the molecule number for each atom for when using LAMMPS
+
 2023.2.6 -- Added handling of OPLS-AA forcefield
    * Added handling of the OPLS-AA forcefield
    * Moved documentation to new MolSSI theme and diátaxis layout

diff --git a/docs/conf.py b/docs/conf.py
@@ -128,6 +128,7 @@
 html_theme_options = {
     "github_url": "https://github.com/molssi-seamm/seamm_ff_util",
     "twitter_url": "https://twitter.com/MolSSI_NSF",
+    "icon_links": [],
     "logo": {
         "image_light": "SEAMM logo.png",
         "image_dark": "SEAMM Inverted 288x181.png",

diff --git a/seamm_ff_util/forcefield.py b/seamm_ff_util/forcefield.py
@@ -2852,9 +2852,16 @@ def eex_atoms(self, eex, configuration):
             x, y, z = xyz
             result.append((x, y, z, index))
 
-        eex["n_atoms"] = len(result)
+        eex["n_atoms"] = n_atoms = len(result)
         eex["n_atom_types"] = len(atom_types)
 
+        # molecule for each atom
+        molecule = eex["molecule"] = [1] * n_atoms
+        molecules = configuration.find_molecules(as_indices=True)
+        for molecule_id, atoms in enumerate(molecules):
+            for atom in atoms:
+                molecule[atom] = molecule_id
+
     def eex_pair(self, eex, configuration):
         """Create the pair (non-bond) portion of the energy expression"""
         logger.debug("In eex_pair")