Make Analysis only particles include ions
Fixes
cc
@@ -280,7 +280,9 @@ class AlchemicalPhaseFactory(object):
checkpoint_interval = self.options['checkpoint_interval']
# Get the solute atoms
if self.options['store_solute_trajectory']:
- solute_atoms = self.topography.solute_atoms
+ # "Solute" is basically just not water. Includes all non-water atoms and ions
+ # Use set union (|) cast back to list to get output
+ solute_atoms = list(frozenset(self.topography.solute_atoms) | frozenset(self.topography.ions_atoms))
if checkpoint_interval == 1:
logger.warning("WARNING! You have specified both a solute-only trajectory AND a checkpoint "
"interval of 1! You are about write the trajectory of the solute twice!\n"
