Delete pickle identifier and species in torch dataset since the whole…

… configuraion is pickled
openkim · Aug 18, 2019 · b3083c1 · b3083c1
1 parent d2724ed
commit b3083c1
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Showing 2 changed files with 5 additions and 17 deletions.
diff --git a/kliff/descriptors/descriptor.py b/kliff/descriptors/descriptor.py
@@ -6,7 +6,6 @@
 import kliff
 from .. import parallel
 from ..log import log_entry
-from ..atomic_data import atomic_number
 
 logger = kliff.logger.get_logger(__name__)
 
@@ -235,10 +234,6 @@ def dump_fingerprints(
                         dzetadr_s = dzetadr_s / stdev_3d
 
                 # pickling data
-                identifier = conf.get_identifier()
-                species = conf.get_species()
-                species = np.asarray([atomic_number[i] for i in species], np.intc)
-                weight = np.asarray(conf.get_weight(), self.dtype)
                 zeta = np.asarray(zeta, self.dtype)
                 energy = np.asarray(conf.get_energy(), self.dtype)
                 if fit_forces:
@@ -249,14 +244,7 @@ def dump_fingerprints(
                     stress = np.asarray(conf.get_stress(), self.dtype)
                     volume = np.asarray(conf.get_volume(), self.dtype)
 
-                example = {
-                    'configuration': conf,
-                    'identifier': identifier,
-                    'species': species,
-                    'weight': weight,
-                    'zeta': zeta,
-                    'energy': energy,
-                }
+                example = {'configuration': conf, 'zeta': zeta, 'energy': energy}
                 if fit_forces:
                     example['dzetadr_forces'] = dzetadr_f
                     example['forces'] = forces

diff --git a/kliff/loss.py b/kliff/loss.py
@@ -774,10 +774,10 @@ def get_loss_single_config(self, sample, pred_energy, pred_forces, pred_stress):
                 pred = pred_stress.reshape(-1)
                 ref = ref_stress.reshape(-1)
 
-        identifier = sample['identifier']
-        species = sample['species']
-        weight = sample['weight']
-        natoms = len(species)
+        conf = sample['configuration']
+        identifier = conf.get_identifier()
+        natoms = conf.get_number_of_atoms()
+        weight = conf.get_weight()
 
         residual = self.residual_fn(
             identifier, natoms, weight, pred, ref, self.residual_data