Add support for using a custom list of lambda values. [closes #41]

src/somd2/config/_config.py

@@ -26,7 +26,7 @@
 __all__ = ["Config"]
 
 
-from collections.abc import Iterable as _Iterable
+from typing import Iterable as _Iterable
 from openmm import Platform as _Platform
 from pathlib import Path as _Path
 
@@ -72,6 +72,11 @@ class Config:
         "log_level": [level.lower() for level in _logger._core.levels],
     }
 
+    # A dictionary of nargs for the various options.
+    _nargs = {
+        "lambda_values": "+",
+    }
+
     def __init__(
         self,
         log_level="info",
@@ -86,6 +91,7 @@ def __init__(
         cutoff="7.5A",
         h_mass_factor=1.5,
         num_lambda=11,
+        lambda_values=None,
         lambda_schedule="standard_morph",
         charge_scale_factor=0.2,
         swap_end_states=False,
@@ -153,6 +159,10 @@ def __init__(
         num_lambda: int
             Number of lambda windows to use.
 
+        lambda_values: [float]
+            A list of lambda values. When specified, this takes precedence over
+            the 'num_lambda' option.
+
         lambda_schedule: str
             Lambda schedule to use for alchemical free energy simulations.
 
@@ -281,6 +291,7 @@ def __init__(
         self.h_mass_factor = h_mass_factor
         self.timestep = timestep
         self.num_lambda = num_lambda
+        self.lambda_values = lambda_values
         self.lambda_schedule = lambda_schedule
         self.charge_scale_factor = charge_scale_factor
         self.swap_end_states = swap_end_states
@@ -616,6 +627,29 @@ def num_lambda(self, num_lambda):
                 raise ValueError("'num_lambda' must be an integer")
         self._num_lambda = num_lambda
 
+    @property
+    def lambda_values(self):
+        return self._lambda_values
+
+    @lambda_values.setter
+    def lambda_values(self, lambda_values):
+        if lambda_values is not None:
+            if not isinstance(lambda_values, _Iterable):
+                raise ValueError("'lambda_values' must be an iterable")
+            try:
+                lambda_values = [float(x) for x in lambda_values]
+            except:
+                raise ValueError("'lambda_values' must be an iterable of floats")
+
+            if not all(0 <= x <= 1 for x in lambda_values):
+                raise ValueError(
+                    "All entries in 'lambda_values' must be between 0 and 1"
+                )
+
+            self._num_lambda = len(lambda_values)
+
+        self._lambda_values = lambda_values
+
     @property
     def lambda_schedule(self):
         return self._lambda_schedule
@@ -1273,6 +1307,12 @@ def _create_parser(cls):
             # Get the type of the parameter. If None, then use str.
             typ = str if params[param].default is None else type(params[param].default)
 
+            # Get the nargs for the parameter.
+            if param in cls._nargs:
+                nargs = cls._nargs[param]
+            else:
+                nargs = None
+
             # This parameter has choices.
             if param in cls._choices:
                 parser.add_argument(
@@ -1297,6 +1337,7 @@ def _create_parser(cls):
                     parser.add_argument(
                         f"--{cli_param}",
                         type=typ,
+                        nargs=nargs,
                         default=params[param].default,
                         help=help[param],
                         required=False,

src/somd2/runner/_runner.py

@@ -62,11 +62,8 @@ def __init__(self, system, config):
             The perturbable system to be simulated. This can be either a path
             to a stream file, or a Sire system object.
 
-        num_lambda: int
-            The number of lambda windows to be simulated.
-
-        platform: str
-            The platform to be used for simulations.
+        config: :class: `Config <somd2.config.Config>`
+            The configuration options for the simulation.
         """
 
         if not isinstance(system, (str, _System)):
@@ -169,10 +166,13 @@ def __init__(self, system, config):
         self._check_end_state_constraints()
 
         # Set the lambda values.
-        self._lambda_values = [
-            round(i / (self._config.num_lambda - 1), 5)
-            for i in range(0, self._config.num_lambda)
-        ]
+        if self._config.lambda_values:
+            self._lambda_values = self._config.lambda_values
+        else:
+            self._lambda_values = [
+                round(i / (self._config.num_lambda - 1), 5)
+                for i in range(0, self._config.num_lambda)
+            ]
 
         # Work out the current hydrogen mass factor.
         h_mass_factor, has_hydrogen = self._get_h_mass_factor(self._system)