From b96a83c1655593f7b1f25177f493d2bc4e3ed366 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Fri, 18 Oct 2024 15:58:32 -0600
Subject: [PATCH] use unyt_arrays for charges and mass instead of lists

---
 gmso/external/convert_hoomd.py | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/gmso/external/convert_hoomd.py b/gmso/external/convert_hoomd.py
index cb777f13..41b51186 100644
--- a/gmso/external/convert_hoomd.py
+++ b/gmso/external/convert_hoomd.py
@@ -284,15 +284,17 @@ def _parse_particle_information(
         site.name if site.atom_type is None else site.atom_type.name
         for site in top.sites
     ]
-    masses = np.zeros(top.n_sites)
-    charges = np.zeros(top.n_sites)
-    for idx, site in enumerate(top.sites):
-        masses[idx] = (
+    masses = u.unyt_array(
+        [
             site.mass.to_value(base_units["mass"])
             if site.mass
             else 1 * base_units["mass"]
-        )
-        charges[idx] = site.charge if site.charge else 0 * u.elementary_charge
+            for site in top.sites
+        ]
+    )
+    charges = u.unyt_array(
+        [site.charge if site.charge else 0 * u.elementary_charge for site in top.sites]
+    )
 
     unique_types = sorted(list(set(types)))
     typeids = np.array([unique_types.index(t) for t in types])
@@ -302,8 +304,9 @@ def _parse_particle_information(
         rigid_ids = [site.molecule.number for site in top.sites]
         rigid_ids_set = set(rigid_ids)
         n_rigid = len(rigid_ids_set)
-        rigid_masses = np.zeros(n_rigid)
-        rigid_xyz = np.zeros((n_rigid, 3))
+        rigid_charges = np.zeros(n_rigid) * charges.units
+        rigid_masses = np.zeros(n_rigid) * masses.units
+        rigid_xyz = np.zeros((n_rigid, 3)) * xyz.units
         # Rigid particle type defaults to "R"; add to front of list
         # TODO: Can we always use "R" here? What if an atom_type is "R"?
         unique_types = ["R"] + unique_types
@@ -322,8 +325,8 @@ def _parse_particle_information(
         # Append rigid center mass and xyz to front
         masses = np.concatenate((rigid_masses, masses))
         xyz = np.concatenate((rigid_xyz, xyz))
-        charges = np.concatenate((np.zeros(n_rigid), charges))
-        rigid_id_tags = np.concatenate((np.arange(n_rigid), np.array(rigid_ids)))
+        charges = np.concatenate((rigid_charges, charges))
+        rigid_id_tags = np.concatenate((np.arange(n_rigid), rigid_ids))
     else:
         n_rigid = 0