Merge pull request #68 from OpenBioSim/fix_67

Fix for #67

Author: lohedges

src/somd2/config/_config.py

@@ -1185,10 +1185,16 @@ def checkpoint_frequency(self, checkpoint_frequency):
         if (
             t.value() < self._energy_frequency.value()
             and t.value() < self._frame_frequency.value()
+            and t.value() > 0
         ):
             _logger.warning(
                 "Checkpoint frequency is low. Should be greater min(energy_frequency, frame_frequency)"
             )
+        if t.value() > self._runtime.value():
+            _logger.debug(
+                "Checkpoint frequency < runtime, checkpointing will not occur before runtime is reached."
+            )
+            t = _sr.u("0ps")
         self._checkpoint_frequency = t
 
     @property

src/somd2/runner/_runner.py

@@ -637,7 +637,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
         else:
             try:
                 dynamics.run(
-                    self._config.checkpoint_frequency,
+                    time,
                     energy_frequency=self._config.energy_frequency,
                     frame_frequency=self._config.frame_frequency,
                     lambda_windows=lambda_array,