From df8477a7db46973bc1b28a2ff93b7f6120cd4ccd Mon Sep 17 00:00:00 2001
From: Seung Hyun Kim <skim449@illinois.edu>
Date: Tue, 25 Jun 2024 09:30:40 -0500
Subject: [PATCH] bug: fix issue that boudnary condition was not properly
 beling applied

---
 elastica/boundary_conditions.py | 18 ++++++++++++------
 elastica/modules/constraints.py |  8 +++++++-
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/elastica/boundary_conditions.py b/elastica/boundary_conditions.py
index 87ce61b2..20c10177 100644
--- a/elastica/boundary_conditions.py
+++ b/elastica/boundary_conditions.py
@@ -11,7 +11,7 @@
 
 from elastica._linalg import _batch_matvec, _batch_matrix_transpose
 from elastica._rotations import _get_rotation_matrix
-from elastica.typing import SystemType, RodType, RigidBodyType
+from elastica.typing import SystemType, RodType, RigidBodyType, ConstrainingIndex
 
 
 S = TypeVar("S")
@@ -34,18 +34,24 @@ class ConstraintBase(ABC, Generic[S]):
     """
 
     _system: S
-    _constrained_position_idx: np.ndarray
-    _constrained_director_idx: np.ndarray
+    _constrained_position_idx: NDArray[np.integer]
+    _constrained_director_idx: NDArray[np.integer]
 
-    def __init__(self, *args: Any, **kwargs: Any) -> None:
+    def __init__(
+        self,
+        *args: Any,
+        constrained_position_idx: ConstrainingIndex,
+        constrained_director_idx: ConstrainingIndex,
+        **kwargs: Any,
+    ) -> None:
         """Initialize boundary condition"""
         try:
             self._system = kwargs["_system"]
             self._constrained_position_idx = np.array(
-                kwargs.get("constrained_position_idx", []), dtype=int
+                constrained_position_idx, dtype=np.int_
             )
             self._constrained_director_idx = np.array(
-                kwargs.get("constrained_director_idx", []), dtype=int
+                constrained_director_idx, dtype=np.int_
             )
         except KeyError:
             raise KeyError(
diff --git a/elastica/modules/constraints.py b/elastica/modules/constraints.py
index 344306b3..2ba907f0 100644
--- a/elastica/modules/constraints.py
+++ b/elastica/modules/constraints.py
@@ -215,7 +215,13 @@ def instantiate(self, system: "RodType | RigidBodyType") -> ConstraintBase:
         )
         try:
             bc = self._bc_cls(
-                *positions, *directors, *self._args, _system=system, **self._kwargs
+                *positions,
+                *directors,
+                *self._args,
+                _system=system,
+                constrained_position_idx=self.constrained_position_idx,
+                constrained_director_idx=self.constrained_director_idx,
+                **self._kwargs,
             )
             return bc
         except (TypeError, IndexError):