Add option to limit size of ring flip region.

Author: lohedges

src/somd2/config/_config.py

@@ -141,6 +141,7 @@ def __init__(
         perturbed_system=None,
         terminal_flip_frequency=None,
         terminal_flip_angle=None,
+        terminal_flip_max_mobile_atoms=None,
         gcmc=False,
         gcmc_frequency=None,
         gcmc_selection=None,
@@ -391,6 +392,11 @@ def __init__(
             ``"180 degrees"``. If None (the default), the angle is determined
             automatically for each group from its geometry.
 
+        terminal_flip_max_mobile_atoms: int or None
+            Maximum number of mobile atoms allowed in a terminal ring group.
+            Groups with more mobile atoms than this threshold are skipped during
+            detection. Defaults to None (no limit).
+
         gcmc: bool
             Whether to perform Grand Canonical Monte Carlo (GCMC) water insertions/deletions.
 
@@ -575,6 +581,7 @@ def __init__(
         self.perturbed_system = perturbed_system
         self.terminal_flip_frequency = terminal_flip_frequency
         self.terminal_flip_angle = terminal_flip_angle
+        self.terminal_flip_max_mobile_atoms = terminal_flip_max_mobile_atoms
         self.gcmc = gcmc
         self.gcmc_frequency = gcmc_frequency
         self.gcmc_selection = gcmc_selection
@@ -2064,6 +2071,26 @@ def terminal_flip_angle(self, terminal_flip_angle):
         else:
             self._terminal_flip_angle = None
 
+    @property
+    def terminal_flip_max_mobile_atoms(self):
+        return self._terminal_flip_max_mobile_atoms
+
+    @terminal_flip_max_mobile_atoms.setter
+    def terminal_flip_max_mobile_atoms(self, terminal_flip_max_mobile_atoms):
+        if terminal_flip_max_mobile_atoms is not None:
+            if not isinstance(terminal_flip_max_mobile_atoms, int):
+                try:
+                    terminal_flip_max_mobile_atoms = int(terminal_flip_max_mobile_atoms)
+                except:
+                    raise ValueError(
+                        "'terminal_flip_max_mobile_atoms' must be of type 'int'"
+                    )
+            if terminal_flip_max_mobile_atoms < 1:
+                raise ValueError(
+                    "'terminal_flip_max_mobile_atoms' must be greater than 0"
+                )
+        self._terminal_flip_max_mobile_atoms = terminal_flip_max_mobile_atoms
+
     @property
     def gcmc(self):
         return self._gcmc

src/somd2/runner/_base.py

@@ -692,7 +692,11 @@ def __init__(self, system, config):
                 if self._config.terminal_flip_angle is not None
                 else None
             )
-            self._terminal_groups = detect_terminal_groups(mols, flip_angle=flip_angle)
+            self._terminal_groups = detect_terminal_groups(
+                mols,
+                flip_angle=flip_angle,
+                max_mobile_atoms=self._config.terminal_flip_max_mobile_atoms,
+            )
 
             if not self._terminal_groups:
                 _logger.warning(

src/somd2/runner/_samplers/_terminal_flip.py

@@ -125,7 +125,7 @@ def _round_to_symmetry_angle(raw_angle, tolerance=10.0):
     return symmetry_angles[min_idx]
 
 
-def detect_terminal_groups(system, flip_angle=None):
+def detect_terminal_groups(system, flip_angle=None, max_mobile_atoms=None):
     """
     Detect terminal ring groups in perturbable molecules using Sire's native
     connectivity.
@@ -151,6 +151,11 @@ def detect_terminal_groups(system, flip_angle=None):
         a float is given it overrides the geometric measurement for all
         groups.
 
+    max_mobile_atoms : int or None
+        Maximum number of mobile atoms allowed in a terminal ring group.
+        Groups with more mobile atoms than this threshold are skipped.
+        Defaults to None (no limit).
+
     Returns
     -------
 
@@ -238,6 +243,14 @@ def detect_terminal_groups(system, flip_angle=None):
                 if not mobile:
                     continue
 
+                # Skip groups with too many mobile atoms.
+                if max_mobile_atoms is not None and len(mobile) > max_mobile_atoms:
+                    _logger.warning(
+                        f"Terminal group at pivot atom {j} has {len(mobile)} mobile "
+                        f"atoms (max_mobile_atoms={max_mobile_atoms}). Skipping group."
+                    )
+                    continue
+
                 # Determine the flip angle for this group.
                 if flip_angle is not None:
                     group_angle = flip_angle