Fixed electron density lattice vector in tar data generator.

Author: NikoOinonen

mlspm/data_generation.py

@@ -210,7 +210,8 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
             if len(sample_list["rots"]) != n_sample:
                 raise ValueError(f"Inconsistent number of rotations in sample list ({len(sample_list['rots'])} != {n_sample})")
 
-            if "rho" in sample_list:
+            use_rho = ("rho" in sample_list) and (sample_list["rho"] is not None)
+            if use_rho:
                 tar_path_rho, name_list_rho = sample_list["rho"]
                 tar_rho = tarfile.open(self.base_path / tar_path_rho, "r")
                 if len(name_list_rho) != n_sample:
@@ -226,11 +227,11 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
                 # Load data from tar(s)
                 rots = sample_list["rots"][i_sample]
                 name_hartree = name_list_hartree[i_sample]
-                pot, lvec, xyzs, Zs = self._get_data(tar_hartree, name_hartree)
+                pot, lvec_pot, xyzs, Zs = self._get_data(tar_hartree, name_hartree)
                 pot *= -1  # Unit conversion, eV -> V
-                if "rho" in sample_list:
+                if use_rho:
                     name_rho = name_list_rho[i_sample]
-                    rho, _, _, _ = self._get_data(tar_rho, name_rho)
+                    rho, lvec_rho, _, _ = self._get_data(tar_rho, name_rho)
 
                 if self._timings:
                     t1 = time.perf_counter()
@@ -241,7 +242,7 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
                 b = np.ndarray(pot.shape, dtype=np.float32, buffer=shm_pot.buf)
                 b[:] = pot[:]
 
-                if "rho" in sample_list:
+                if use_rho:
                     sample_id_rho = f"{i_proc}_{proc_id}_{i_sample}_rho"
                     shm_rho = mp.shared_memory.SharedMemory(create=True, size=rho.nbytes, name=sample_id_rho)
                     b = np.ndarray(rho.shape, dtype=np.float32, buffer=shm_rho.buf)
@@ -250,12 +251,13 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
                 else:
                     sample_id_rho = None
                     rho_shape = None
+                    lvec_rho = None
 
                 if self._timings:
                     t2 = time.perf_counter()
 
                 # Inform the main process of the data using the queue
-                self.q.put((i_proc, sample_id_pot, sample_id_rho, pot.shape, rho_shape, lvec, xyzs, Zs, rots))
+                self.q.put((i_proc, sample_id_pot, sample_id_rho, pot.shape, rho_shape, lvec_pot, lvec_rho, xyzs, Zs, rots))
 
                 if self._timings:
                     t3 = time.perf_counter()
@@ -271,7 +273,7 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
                 # Done with shared memory
                 shm_pot.close()
                 shm_pot.unlink()
-                if "rho" in sample_list:
+                if use_rho:
                     shm_rho.close()
                     shm_rho.unlink()
 
@@ -283,7 +285,7 @@ def _load_samples(self, sample_lists: list[TarSampleList], i_proc: int, event: m
                     )
 
             tar_hartree.close()
-            if "rho" in sample_list:
+            if use_rho:
                 tar_rho.close()
 
     def _yield_samples(self):
@@ -294,16 +296,16 @@ def _yield_samples(self):
                 t0 = time.perf_counter()
 
             # Get data info from the queue
-            i_proc, sample_id_pot, sample_id_rho, pot_shape, rho_shape, lvec, xyzs, Zs, rots = self.q.get(timeout=200)
+            i_proc, sample_id_pot, sample_id_rho, pot_shape, rho_shape, lvec_pot, lvec_rho, xyzs, Zs, rots = self.q.get(timeout=200)
 
             # Get data from the shared memory
             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 = HartreePotential(pot, lvec_pot)
             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 = ElectronDensity(rho, lvec_rho)
             else:
                 rho = None
 

tests/test_data_generation.py

@@ -98,15 +98,15 @@ def test_tar_data_generator():
             rots.append([rot])
             names.append(name)
 
-    sample_list = [
+    sample_list_fdbm = [
         {
             "hartree": (tar_path_hartree, names),
             "rho": (tar_path_rho, names),
             "rots": rots,
         }
     ]
 
-    generator = TarDataGenerator(sample_list, base_path='./', n_proc=1)
+    generator = TarDataGenerator(sample_list_fdbm, base_path='./', n_proc=1)
 
     for i_sample, sample in enumerate(generator):
         assert np.allclose(sample['xyzs'], xyzs[i_sample])
@@ -117,5 +117,23 @@ def test_tar_data_generator():
         assert np.allclose(sample['rho_sample'].array, rhos[i_sample])
         assert np.allclose(sample['rho_sample'].lvec, lvecs[i_sample])
 
+
+    sample_list_hartree = [
+        {
+            "hartree": (tar_path_hartree, names),
+            "rho": None,
+            "rots": rots,
+        }
+    ]
+
+    generator = TarDataGenerator(sample_list_hartree, base_path='./', n_proc=1)
+
+    for i_sample, sample in enumerate(generator):
+        assert np.allclose(sample['xyzs'], xyzs[i_sample])
+        assert np.allclose(sample['Zs'], Zs[i_sample])
+        assert np.allclose(sample['rot'], rots[i_sample])
+        assert np.allclose(sample['qs'].array, -hartrees[i_sample])
+        assert np.allclose(sample['qs'].lvec, lvecs[i_sample])
+
     tar_path_hartree.unlink()
     tar_path_rho.unlink()