Merge pull request #135 from OpenBioSim/feature_taylor

Expose Taylor softcore options and pass through to Loch

Author: lohedges

src/somd2/config/_config.py

@@ -151,6 +151,7 @@ def __init__(
         rest2_scale=1.0,
         rest2_selection=None,
         softcore_form="zacharias",
+        taylor_power=1,
         output_directory="output",
         restart=False,
         use_backup=False,
@@ -438,6 +439,11 @@ def __init__(
             The soft-core potential form to use for alchemical interactions. This can be
             either "zacharias" or "taylor". The default is "zacharias".
 
+        taylor_power: int
+            The power to use for the alpha term in the Taylor soft-core LJ expression,
+            i.e. sig6 = sigma^6 / (alpha^m * sigma^6 + r^6). Must be between 0 and 4.
+            The default is 1. Only used when softcore_form is "taylor".
+
         output_directory: str
             Path to a directory to store output files.
 
@@ -567,6 +573,7 @@ def __init__(
         self.restart = restart
         self.use_backup = use_backup
         self.softcore_form = softcore_form
+        self.taylor_power = taylor_power
         self.somd1_compatibility = somd1_compatibility
         self.pert_file = pert_file
         self.save_crash_report = save_crash_report
@@ -2204,6 +2211,21 @@ def softcore_form(self, softcore_form):
         else:
             self._softcore_form = softcore_form
 
+    @property
+    def taylor_power(self):
+        return self._taylor_power
+
+    @taylor_power.setter
+    def taylor_power(self, taylor_power):
+        if not isinstance(taylor_power, int):
+            try:
+                taylor_power = int(taylor_power)
+            except Exception:
+                raise ValueError("'taylor_power' must be of type 'int'")
+        if not 0 <= taylor_power <= 4:
+            raise ValueError("'taylor_power' must be between 0 and 4")
+        self._taylor_power = taylor_power
+
     @property
     def use_backup(self):
         return self._use_backup

src/somd2/runner/_base.py

@@ -209,6 +209,7 @@ def __init__(self, system, config):
         # If specified, use the Taylor soft-core form.
         if self._config.softcore_form == "taylor":
             self._config._extra_args["use_taylor_softening"] = True
+            self._config._extra_args["taylor_power"] = self._config.taylor_power
 
         # We're running in SOMD1 compatibility mode.
         if self._config.somd1_compatibility:
@@ -769,6 +770,8 @@ def __init__(self, system, config):
                 "radius": str(self._config.gcmc_radius),
                 "reference": self._config.gcmc_selection,
                 "restart": self._is_restart,
+                "softcore_form": self._config.softcore_form,
+                "taylor_power": self._config.taylor_power,
                 "standard_volume": str(self._config.gcmc_standard_volume),
                 "tolerance": self._config.gcmc_tolerance,
             }