rename DlPolyHistory class

popelier-group · May 16, 2024 · 3c7bcfd · 3c7bcfd
1 parent 4ca47cd
commit 3c7bcfd
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Showing 7 changed files with 17 additions and 17 deletions.
diff --git a/docs/source/ichor_core_examples/working_with_ichor_files.ipynb b/docs/source/ichor_core_examples/working_with_ichor_files.ipynb
@@ -12,7 +12,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -30,7 +30,7 @@
        " 'OrcaEngrad',\n",
        " 'OrcaOutput',\n",
        " 'Trajectory',\n",
-       " 'DlpolyHistory',\n",
+       " 'DlPolyHistory',\n",
        " 'DlPolyField',\n",
        " 'DlPolyConfig',\n",
        " 'DlPolyControl',\n",
@@ -49,7 +49,7 @@
        " 'PandoraDirectory']"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 1,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -145,7 +145,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [

diff --git a/ichor_core/ichor/core/analysis/dlpoly/true_vs_predicted.py b/ichor_core/ichor/core/analysis/dlpoly/true_vs_predicted.py
@@ -29,7 +29,7 @@
 
 import numpy as np
 from ichor.core.files import PointsDirectory, Trajectory
-from ichor.core.files.dl_poly import DlPolyFFLUX, DlpolyHistory
+from ichor.core.files.dl_poly import DlPolyFFLUX, DlPolyHistory
 from matplotlib import pyplot as plt
 
 ascii_uppercase = list(ascii_uppercase)
@@ -45,7 +45,7 @@ def r2_score(true, predicted):
 
 
 def get_random_geometries_from_fflux_simulation(
-    history: Union[DlpolyHistory, Path, str],
+    history: Union[DlPolyHistory, Path, str],
     k: int = 1000,
     fflux_file: Union[DlPolyFFLUX, Path, str] = None,
 ):
@@ -68,7 +68,7 @@ def get_random_geometries_from_fflux_simulation(
     """
 
     if isinstance(history, (Path, str)):
-        history = DlpolyHistory(history)
+        history = DlPolyHistory(history)
 
     random_indices = random.sample(range(len(history)), k=1000)
 

diff --git a/ichor_core/ichor/core/analysis/trajectory_analysis.py b/ichor_core/ichor/core/analysis/trajectory_analysis.py
@@ -5,7 +5,7 @@
 import numpy as np
 from ichor.core.calculators import default_connectivity_calculator
 from ichor.core.common.pairwise import pairwise
-from ichor.core.files import DlpolyHistory, GJF, Trajectory, XYZ
+from ichor.core.files import DlPolyHistory, GJF, Trajectory, XYZ
 from ichor.core.files.file import ReadFile
 
 # TODO: potentially move Distance to outside of models/kernels
@@ -37,7 +37,7 @@ def __init__(self, trajectory_path: Union[Path, str]):
         self.trajectory = (
             Trajectory(trajectory_path)
             if trajectory_path.suffix == ".xyz"
-            else DlpolyHistory(trajectory_path)
+            else DlPolyHistory(trajectory_path)
         )
         self.distances_vectors = self._compute_distances_vectors()
         self._bond_lengths_matrix = None

diff --git a/ichor_core/ichor/core/files/__init__.py b/ichor_core/ichor/core/files/__init__.py
@@ -7,7 +7,7 @@
     DlPolyControl,
     DlPolyFFLUX,
     DlPolyField,
-    DlpolyHistory,
+    DlPolyHistory,
     DlPolyIQAEnergies,
     DlPolyIQAForces,
     FFLUXDirectory,
@@ -52,7 +52,7 @@
     "OrcaEngrad",
     "OrcaOutput",
     "Trajectory",
-    "DlpolyHistory",
+    "DlPolyHistory",
     "DlPolyField",
     "DlPolyConfig",
     "DlPolyControl",

diff --git a/ichor_core/ichor/core/files/dl_poly/__init__.py b/ichor_core/ichor/core/files/dl_poly/__init__.py
@@ -2,7 +2,7 @@
 from ichor.core.files.dl_poly.dl_poly_control import DlPolyControl
 from ichor.core.files.dl_poly.dl_poly_fflux import DlPolyFFLUX
 from ichor.core.files.dl_poly.dl_poly_field import DlPolyField
-from ichor.core.files.dl_poly.dl_poly_history import DlpolyHistory
+from ichor.core.files.dl_poly.dl_poly_history import DlPolyHistory
 from ichor.core.files.dl_poly.dl_poly_iqa_energies import DlPolyIQAEnergies
 from ichor.core.files.dl_poly.dl_poly_iqa_forces import DlPolyIQAForces
 from ichor.core.files.dl_poly.fflux_directory import FFLUXDirectory
@@ -11,7 +11,7 @@
     "DlPolyConfig",
     "DlPolyControl",
     "DlPolyField",
-    "DlpolyHistory",
+    "DlPolyHistory",
     "DlPolyIQAEnergies",
     "DlPolyIQAForces",
     "DlPolyFFLUX",

diff --git a/ichor_core/ichor/core/files/dl_poly/dl_poly_history.py b/ichor_core/ichor/core/files/dl_poly/dl_poly_history.py
@@ -93,7 +93,7 @@ def __init__(self):
         self.timestep = None
 
 
-class DlpolyHistory(Trajectory):
+class DlPolyHistory(Trajectory):
     """
     DLPOLY HISTORY File
 

diff --git a/ichor_core/ichor/core/files/dl_poly/fflux_directory.py b/ichor_core/ichor/core/files/dl_poly/fflux_directory.py
@@ -2,7 +2,7 @@
 from ichor.core.files.directory import AnnotatedDirectory
 from ichor.core.files.dl_poly import (
     DlPolyFFLUX,
-    DlpolyHistory,
+    DlPolyHistory,
     DlPolyIQAEnergies,
     DlPolyIQAForces,
 )
@@ -19,7 +19,7 @@ class FFLUXDirectory(AnnotatedDirectory):
         "fflux_file": DlPolyFFLUX,
         "iqa_energies_file": DlPolyIQAEnergies,
         "iqa_forces_file": DlPolyIQAForces,
-        "history_file": DlpolyHistory,
+        "history_file": DlPolyHistory,
     }
 
     @property