dyn: cell dynamics with vectors

miniff/dyn.py

@@ -103,7 +103,7 @@ class DynCell(Cell):
 
     @property
     def cell_velocity(self):
-        return self.meta.get("cell_velocity", None)
+        return self.meta.get("cell-velocity", None)
 
     @property
     def masses(self):
@@ -124,7 +124,7 @@ class DynCell(Cell):
     def copy(self, cartesian_velocity=None, cell_velocity=None, masses=None, time=None, **kwargs):
         result = super().copy(**kwargs)
         d = locals()
-        for i, j in (("cartesian_velocity", "velocities"), ("cell_velocity",) * 2, ("masses",) * 2, ("time",) * 2):
+        for i, j in (("cartesian_velocity", "velocities"), ("cell_velocity", "cell-velocity"), ("masses",) * 2, ("time",) * 2):
             if d[i] is not None:
                 result.meta[j] = d[i]
         return result
@@ -249,8 +249,7 @@ class DynWrapper:
 
         ndims = self.state.vectors.shape[0]
         mass = np.repeat(self.state.masses[:, None], ndims, 1).reshape(-1)
-        gc = self.state.gc
-        gc = np.concatenate([gc.coordinates.cartesian.reshape(-1), gc.velocities.cartesian.reshape(-1)])
+        gc = self.wrapper.c2p(self.state.gc)
         t0 = self.state.time
         result = driver(lambda _, x: eom(self.wrapper, x, mass), (0, time), gc, **kwargs)
         if snapshots:

miniff/kernel.py

@@ -816,11 +816,11 @@ class ScalarFunctionWrapper:
                     raise ValueError("One or more potentials do not include the 'fidelity' kernel")
         self.compute_images_kwargs = {"cutoff": max(i.cutoff for i in potentials), **kwargs}
 
-    def p2c(self, parameters: np.ndarray) -> sf_parameters:
+    def p2c(self, parameters: np.ndarray):
         """Unpacks parameters."""
         return sf_parameters.unpack(parameters.reshape(-1, 3), **self.include)
 
-    def c2p(self, coordinates: sf_parameters) -> np.ndarray:
+    def c2p(self, coordinates) -> np.ndarray:
         """Packs parameters."""
         return coordinates.copy(**self.include).pack().reshape(-1)