unsampled endstates long range correction as an input yaml option (#1037

)

* Support for unsampled endstates long range correction as an input yaml option

* Changes in release notes and YAML file for the protein-ligand cli example.

* Better wording for changelog.

* Applying suggestions. Remove unused option. Commenting new options.

docs/changelog.rst

@@ -8,6 +8,13 @@ This section lists features and improvements of note in each release.
 
 The full release history can be viewed `at the GitHub perses releases page <https://github.com/choderalab/perses/releases>`_.
 
+0.10.0 - Release
+----------------
+
+Enhancements
+------------
+- Introduce ``unsampled_endstates`` boolean option in input YAML file, for enabling/disabling creation of unsampled endstates long-range sterics correction. Issue `#1033 <https://github.com/choderalab/perses/issues/1033>`_ (`#1037 <https://github.com/choderalab/perses/pull/1037>`_).
+
 0.9.5 - Release
 ---------------
 

examples/protein-ligand/cli/protein-ligand.yaml

@@ -46,7 +46,7 @@ fe_type: repex
 checkpoint_interval: 50 
 
 #number of iterations
-n_cycles: 1
+n_cycles: 4
 
 #The number of SAMS states
 n_states: 3
@@ -72,4 +72,8 @@ phases:
 #timestep in fs
 timestep: 4.
 
-h_constraints: True
+# Interval in iterations to use for offline real time analysis
+offline-freq: 2
+
+# Create unsampled endstates for long-range sterics correction
+unsampled_endstates: True

perses/app/setup_relative_calculation.py

@@ -326,6 +326,10 @@ def getSetupOptions(filename, override_string=None):
     if 'platform' not in setup_options:
         setup_options['platform'] = None  # defaults to choosing best platform
 
+    # Handling unsampled_endstates long range correction flag
+    if 'unsampled_endstates' not in setup_options:
+        setup_options['unsampled_endstates'] = True   # True by default (matches class default)
+
     os.makedirs(trajectory_directory, exist_ok=True)
 
 
@@ -658,10 +662,7 @@ def run_setup(setup_options, serialize_systems=True, build_samplers=True):
                 if phase == 'vacuum':
                     endstates = False
                 else:
-                    # TODO: Make this True when dispersed.utils.create_endstates is fixed
-                    _logger.info("Disabling creation of endstates with expanded cutoffs in order to support new "
-                                 "alchemical factories.")
-                    endstates = False
+                    endstates = setup_options['unsampled_endstates']
 
                 if setup_options['fe_type'] == 'fah':
                     _logger.info('SETUP FOR FAH DONE')