Update potential/density buffers without reallocation.

Author: NikoOinonen

mlspm/data_generation.py

@@ -165,6 +165,8 @@ def __init__(self, samples: list[TarSampleList], base_path: PathLike = "./", n_p
         self.samples = samples
         self.base_path = Path(base_path)
         self.n_proc = n_proc
+        self.pot = None
+        self.rho = None
 
     def __len__(self) -> int:
         """Total number of samples (including rotations)"""
@@ -292,24 +294,40 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
 
     def _get_queue_sample(self):
 
+        if self._timings:
+            t0 = time.perf_counter()
+
         i_proc, sample_id_pot, sample_id_rho, pot_shape, rho_shape, lvec_pot, lvec_rho, xyzs, Zs, rots = self.q.get(timeout=200)
 
+        if self._timings:
+            t1 = time.perf_counter()
+
         shm_pot = mp.shared_memory.SharedMemory(sample_id_pot)
         pot = np.ndarray(pot_shape, dtype=np.float32, buffer=shm_pot.buf)
-        pot = HartreePotential(pot, lvec_pot)
-        # This starts a copy to the OpenCL device. Better to start it here so that buffer preparation is instant during the simulation.
-        pot.cl_array
+        if self.pot is None:
+            self.pot = HartreePotential(pot, lvec_pot)
+        else:
+            self.pot.update_array(pot, lvec_pot)
+
+        if self._timings:
+            t2 = time.perf_counter()
 
         if sample_id_rho is not None:
             shm_rho = mp.shared_memory.SharedMemory(sample_id_rho)
             rho = np.ndarray(rho_shape, dtype=np.float32, buffer=shm_rho.buf)
-            rho = ElectronDensity(rho, lvec_rho)
-            rho.cl_array
+            if self.rho is None:
+                self.rho = ElectronDensity(rho, lvec_rho)
+            else:
+                self.rho.update_array(pot, lvec_pot)
         else:
             shm_rho = None
             rho = None
 
-        return i_proc, xyzs, Zs, rots, pot, shm_pot, rho, shm_rho, sample_id_pot
+        if self._timings:
+            t3 = time.perf_counter()
+            print(f"[Main, receive data, id {sample_id_pot}] Queue / Pot / Rho: " f"{t1 - t0:.5f} / {t2 - t1:.5f} / {t3 - t2:.5f}")
+
+        return i_proc, xyzs, Zs, rots, self.pot, shm_pot, self.rho, shm_rho, sample_id_pot
 
     def _yield_samples(self):