Moredocs nico

apax/md/io.py

@@ -50,7 +50,7 @@ def atoms_from_state(self, state, energy, nbr_kwargs):
 
         atoms = Atoms(self.atomic_numbers, positions, momenta=momenta, cell=box)
         atoms.cell = atoms.cell.T
-        atoms.pbc = np.diag(atoms.cell.array) > 1e-7
+        atoms.pbc = np.diag(atoms.cell.array) > 1e-6
         atoms.calc = SinglePointCalculator(atoms, energy=float(energy), forces=forces)
         return atoms
 
@@ -66,7 +66,7 @@ def __init__(
     ) -> None:
         self.atomic_numbers = system.atomic_numbers
         self.box = system.box
-        self.fractional = np.any(self.box < 1e-6)
+        self.fractional = np.any(self.box > 1e-6)
         self.sampling_rate = sampling_rate
         self.traj_path = traj_path
         self.db = znh5md.io.DataWriter(self.traj_path)

apax/md/nvt.py

@@ -339,8 +339,10 @@ def md_setup(model_config: Config, md_config: MDConfig):
     r_max = model_config.model.r_max
     log.info("initializing model")
     if np.all(system.box < 1e-6):
+        frac_coords = False
         displacement_fn, shift_fn = space.free()
     else:
+        frac_coords = True
         heights = heights_of_box_sides(system.box)
 
         if np.any(atoms.cell.lengths() / 2 < r_max):
@@ -356,7 +358,7 @@ def md_setup(model_config: Config, md_config: MDConfig):
                 "can not calculate the correct neighbors",
             )
         displacement_fn, shift_fn = space.periodic_general(
-            system.box, fractional_coordinates=True
+            system.box, fractional_coordinates=frac_coords
         )
 
     builder = ModelBuilder(model_config.model.get_dict())
@@ -368,7 +370,7 @@ def md_setup(model_config: Config, md_config: MDConfig):
         system.box,
         r_max,
         md_config.dr_threshold,
-        fractional_coordinates=True,
+        fractional_coordinates=frac_coords,
         format=partition.Sparse,
         disable_cell_list=True,
     )

apax/train/eval.py

@@ -36,7 +36,13 @@ def load_test_data(
 ):  # TODO double code run.py in progress
     log.info("Running Input Pipeline")
     os.makedirs(eval_path, exist_ok=True)
-    if config.data.data_path is not None:
+
+    if config.data.test_data_path is not None:
+        log.info(f"Read test data file {config.data.test_data_path}")
+        atoms_list = load_data(config.data.test_data_path)
+        atoms_list = atoms_list[:n_test]
+
+    elif config.data.data_path is not None:
         log.info(f"Read data file {config.data.data_path}")
         atoms_list = load_data(config.data.data_path)
 
@@ -54,12 +60,6 @@ def load_test_data(
 
         atoms_list, _ = split_atoms(atoms_list, test_idxs)
 
-    elif config.data.test_data_path is not None:
-        log.info(f"Read test data file {config.data.test_data_path}")
-        atoms_list, label_dict = load_data(config.data.test_data_path)
-        atoms_list = atoms_list[:n_test]
-        for key, val in label_dict.items():
-            label_dict[key] = val[:n_test]
     else:
         raise ValueError("input data path/paths not defined")
 
@@ -80,6 +80,7 @@ def predict(model, params, Metrics, loss_fn, test_ds, callbacks, is_ensemble=Fal
         0, test_ds.n_data, desc="Structure", ncols=100, disable=False, leave=True
     )
     for batch_idx in range(test_ds.n_data):
+        callbacks.on_test_batch_begin(batch_idx)
         batch = next(batch_test_ds)
         batch_start_time = time.time()
 

apax/utils/datasets.py

@@ -36,6 +36,23 @@ def download_benzene_DFT(data_path):
     return new_file_path
 
 
+def download_etoh_ccsdt(data_path):
+    url = "http://www.quantum-machine.org/gdml/data/xyz/ethanol_ccsd_t.zip"
+    file_path = data_path / "ethanol_ccsd_t.zip"
+
+    os.makedirs(data_path, exist_ok=True)
+    urllib.request.urlretrieve(url, file_path)
+
+    with zipfile.ZipFile(file_path, "r") as zip_ref:
+        zip_ref.extractall(data_path)
+
+    test_file_path = data_path / "ethanol_ccsd_t-test.xyz"
+    train_file_path = data_path / "ethanol_ccsd_t-train.xyz"
+    os.remove(file_path)
+
+    return train_file_path, test_file_path
+
+
 def download_md22_benzene_CCSDT(data_path):
     url = "http://www.quantum-machine.org/gdml/data/xyz/benzene_ccsd_t.zip"
     file_path = data_path / "benzene_ccsdt.zip"

apax/utils/helpers.py

@@ -1,4 +1,5 @@
 import yaml
+import csv
 
 
 def setup_ase():
@@ -17,8 +18,33 @@ def mod_config(config_path, updated_config):
         config_dict = yaml.safe_load(stream)
 
     for key, new_value in updated_config.items():
-        if isinstance(config_dict[key], dict):
-            config_dict[key].update(new_value)
+        if key in config_dict.keys():
+            if isinstance(config_dict[key], dict):
+                config_dict[key].update(new_value)
+            else:
+                config_dict[key] = new_value
         else:
             config_dict[key] = new_value
     return config_dict
+
+
+def load_csv_metrics(path):
+    data_dict = {}
+
+    with open(path, "r") as file:
+        reader = csv.reader(file)
+
+        # Extract the headers (keys) from the first row
+        headers = next(reader)
+
+        # Initialize empty lists for each key
+        for header in headers:
+            data_dict[header] = []
+
+        # Read the rest of the rows and append values to the corresponding key
+        for row in reader:
+            for idx, value in enumerate(row):
+                key = headers[idx]
+                data_dict[key].append(float(value))
+
+    return data_dict