From c7c734781cc3a75d98b6dcb3c9c383e67b6cc032 Mon Sep 17 00:00:00 2001
From: chrisjonesBSU <chrisjones4@u.boisestate.edu>
Date: Thu, 6 Mar 2025 12:15:04 -0700
Subject: [PATCH] add local changes

---
 flowermd/base/simulation.py     | 23 ++++++++++++-----------
 flowermd/library/forcefields.py | 13 ++++++++++++-
 2 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/flowermd/base/simulation.py b/flowermd/base/simulation.py
index e05d99c3..d02eba14 100644
--- a/flowermd/base/simulation.py
+++ b/flowermd/base/simulation.py
@@ -13,7 +13,7 @@
 import numpy as np
 import unyt as u
 
-from flowermd.internal import validate_ref_value
+from flowermd.internal import check_return_iterable, validate_ref_value
 from flowermd.utils.actions import StdOutLogger, UpdateWalls
 from flowermd.utils.base_types import HOOMDThermostats
 
@@ -52,7 +52,7 @@ class Simulation(hoomd.simulation.Simulation):
     thermostat : flowermd.utils.HOOMDThermostats, default
         HOOMDThermostats.MTTK
         The thermostat to use for the simulation.
-    constraint : hoomd.md.constrain object
+    constraint : list of hoomd.md.constrain objects
         Sets constraints for the simulation.
         See flowermd.utils.constraints for built-in helpers
         or see https://hoomd-blue.readthedocs.io/en/stable/hoomd/md/module-constrain.html
@@ -108,17 +108,18 @@ def __init__(
         self._dt = dt
         self._reference_values = dict()
         self._reference_values = reference_values
-        self.constraint = constraint
+        self.constraint = check_return_iterable(constraint)
         self._rigid_constraint = None
         self._distance_constraint = None
-        if constraint and isinstance(constraint, hoomd.md.constrain.Rigid):
-            self._rigid_constraint = constraint
-        elif constraint and isinstance(constraint, hoomd.md.constrain.Distance):
-            self._distance_constraint = constraint
-        elif constraint:
-            raise ValueError(
-                "`constaint` must be an instance of hoomd.md.constrain."
-            )
+        for obj in self.constraint:
+            if isinstance(obj, hoomd.md.constrain.Rigid):
+                self._rigid_constraint = obj
+            elif isinstance(obj, hoomd.md.constrain.Distance):
+                self._distance_constraint = obj
+            else:
+                raise ValueError(
+                    "`constaint` must be an instance of hoomd.md.constrain."
+                )
         self._integrate_group = self._create_integrate_group(
             rigid=True if self._rigid_constraint else False
         )
diff --git a/flowermd/library/forcefields.py b/flowermd/library/forcefields.py
index 2f28ee22..9a138710 100644
--- a/flowermd/library/forcefields.py
+++ b/flowermd/library/forcefields.py
@@ -618,6 +618,7 @@ def _create_forcefield(self):
                 k=self.angle_k, t0=self.angle_theta0
             )
             angle.params["_H-_C-_H"] = dict(k=0, t0=0)
+            # angle.params["_H-_C-_T"] = dict(k=0, t0=0)
             forces.append(angle)
         # Gay-Berne Pairs
         nlist = hoomd.md.nlist.Cell(buffer=0.40)
@@ -626,7 +627,17 @@ def _create_forcefield(self):
             epsilon=self.epsilon, lperp=self.lperp, lpar=self.lpar
         )
         # Add zero pairs
-        for pair in [("_H", "_H"), ("_C", "_H")]:
+        for pair in [
+            ("_H", "_H"),
+            ("_T", "_T"),
+            ("R", "R"),
+            ("_C", "_H"),
+            ("_C", "_T"),
+            ("_C", "R"),
+            ("_T", "_H"),
+            ("_T", "R"),
+            ("_H", "R"),
+        ]:
             gb.params[pair] = dict(epsilon=0.0, lperp=0.0, lpar=0.0)
             gb.params[pair].r_cut = 0.0
         forces.append(gb)