bugfix-ncycles-computed

a3fe/_version.py

@@ -1 +1 @@
-__version__ = "0.4.1"
+__version__ = "0.4.2"

a3fe/configuration/engine_config.py

@@ -117,9 +117,13 @@ class SomdConfig(_EngineConfig):
 
     ### Integrator - ncycles modified as required by a3fe ###
     timestep: float = _Field(4.0, description="Timestep in femtoseconds(fs)")
+    nmoves: int = _Field(
+        25000,
+        description="Number of moves per cycle. Default 25000 provides optimal checkpoint frequency.",
+    )
     runtime: _Union[int, float] = _Field(
         5.0,
-        description="Runtime in nanoseconds(ns), and must be a multiple of timestep",
+        description="Runtime in nanoseconds(ns), must be a multiple of timestep and ncycles will be calculated from runtime and nmoves",
     )
 
     ### Constraints ###
@@ -225,29 +229,37 @@ class SomdConfig(_EngineConfig):
     )
 
     @property
-    def nmoves(self) -> int:
+    def ncycles(self) -> int:
         """
-        Make sure runtime is a multiple of timestep
+        Calculate number of cycles from runtime, nmoves and timestep.
+        Formula: runtime = nmoves × ncycles × timestep
         """
         # Convert runtime to femtoseconds (ns -> fs)
         runtime_fs = _Decimal(str(self.runtime)) * _Decimal("1_000_000")
         timestep = _Decimal(str(self.timestep))
+        nmoves_dec = _Decimal(str(self.nmoves))
 
         # Check if runtime is a multiple of timestep
         remainder = runtime_fs % timestep
         if round(float(remainder), 4) != 0:
             raise ValueError(
-                (
-                    "Runtime must be a multiple of the timestep. "
-                    f"Runtime is {self.runtime} ns ({runtime_fs} fs), "
-                    f"and timestep is {self.timestep} fs."
-                )
+                f"Runtime must be a multiple of timestep. "
+                f"Runtime is {self.runtime} ns ({runtime_fs} fs), "
+                f"timestep is {self.timestep} fs."
             )
 
-        # Calculate the number of moves
-        nmoves = round(float(runtime_fs) / float(timestep))
+        # Calculate ncycles
+        total_steps = runtime_fs / timestep
+        ncycles = total_steps / nmoves_dec
+        ncycles_int = round(float(ncycles))
+
+        if ncycles_int < 1:
+            raise ValueError(
+                f"Runtime {self.runtime} ns is too short for nmoves={self.nmoves}. "
+                f"Decrease nmoves or increase runtime."
+            )
 
-        return nmoves
+        return ncycles_int
 
     @_model_validator(mode="after")
     def _check_rf_dielectric(self):
@@ -336,6 +348,7 @@ def write_config(
         config_lines = [
             "### Integrator ###",
             f"timestep = {self.timestep} * femtosecond",
+            f"ncycles = {self.ncycles}",
             f"nmoves = {self.nmoves}",
             f"constraint = {self.constraint}",
             f"hydrogen mass repartitioning factor = {self.hydrogen_mass_factor}",

a3fe/tests/test_engine_configuration.py

@@ -106,6 +106,44 @@ def test_charge_cutoff_validation(engine_config, charge, cutoff, should_pass):
             engine_config(ligand_charge=charge, cutoff_type=cutoff, runtime=1)
 
 
+@pytest.mark.parametrize(
+    "runtime,nmoves,timestep,calculated_ncycles",
+    [
+        (5.0, 25000, 4.0, 50),
+        (10.0, 50000, 2.0, 100),
+    ],
+)
+def test_ncycles_calculation(
+    somd_engine_config, runtime, nmoves, timestep, calculated_ncycles
+):
+    """Test that ncycles is correctly calculated from runtime, nmoves and timestep."""
+    config = somd_engine_config(runtime=runtime, nmoves=nmoves, timestep=timestep)
+    assert config.ncycles == calculated_ncycles
+
+
+def test_ncycles_invalid_runtime(somd_engine_config):
+    """Test that ValueError is raised when runtime is not a multiple of timestep."""
+    config = somd_engine_config(runtime=5.0, nmoves=25000, timestep=3.0)
+    with pytest.raises(ValueError, match="Runtime must be a multiple of timestep"):
+        config.ncycles
+
+
+def test_ncycles_too_short(somd_engine_config):
+    """Test that ValueError is raised when runtime is too short."""
+    config = somd_engine_config(runtime=0.01, nmoves=25000, timestep=4.0)
+    with pytest.raises(ValueError, match="too short"):
+        config.ncycles
+
+
+def test_ncycles_updates_on_runtime_change(somd_engine_config):
+    """Test that ncycles updates when runtime is changed (SSOT consistency)."""
+    config = somd_engine_config(runtime=5.0, nmoves=25000, timestep=4.0)
+    assert config.ncycles == 50
+
+    config.runtime = 10.0
+    assert config.ncycles == 100
+
+
 def test_ligand_charge_validation(engine_config):
     """Test that ligand charge validation works correctly."""
 

docs/CHANGELOG.rst

@@ -2,6 +2,10 @@
 Change Log
 ===============
 
+0.4.2
+====================
+- Added nmoves as a configurable field and changed ncycles to a computed property in engine_config.py to prevent memory overflow from single-cycle runtimes.
+
 0.4.1
 ====================
 - Fixed the statistical inefficiency timestep units from femtoseconds to nanoseconds.