Fixed the issue of v0's output differing from the original implementa…

…tion.

anisoap/representations/ellipsoidal_density_projection.py

@@ -448,9 +448,9 @@ def __init__(
         # Currently, gradients are not supported
         if compute_gradients:
             raise NotImplementedError(
-                "Sorry! Gradients have not yet been implemented")
-        #
-
+                "Sorry! Gradients have not yet been implemented"
+            )
+        
         # Initialize the radial basis class
         if radial_basis_name not in ["monomial", "gto"]:
             raise NotImplementedError(
@@ -459,7 +459,8 @@ def __init__(
             )
         if radial_gaussian_width != None and radial_basis_name != "gto":
             raise ValueError(
-                "Gaussian width can only be provided with GTO basis")
+                "Gaussian width can only be provided with GTO basis"
+            )
         elif radial_gaussian_width is None and radial_basis_name == "gto":
             raise ValueError("Gaussian width must be provided with GTO basis")
         elif type(radial_gaussian_width) == int:
@@ -529,8 +530,6 @@ def transform(self, frames, show_progress=False, normalize=True, *, version: int
 
         # Define variables determining size of feature vector coming from frames
         self.num_atoms_per_frame = np.array([len(frame) for frame in frames])
-
-        num_particle_types = len(species)
 
         # Initialize arrays in which to store all features
         self.feature_gradients = 0
@@ -567,11 +566,7 @@ def transform(self, frames, show_progress=False, normalize=True, *, version: int
                     frames[i].arrays["c_diameter[3]"][j] / 2,
                 ]
 
-        # TypeError: NeighborList.__init__() takes 3 positional arguments but 4 were given
-        # Deleted the last "True" to resolve this error
-        # NeighborList(self.cutoff_radius, True, True) -> NeighborList(self.cutoff_radius, True)
-        self.nl = NeighborList(
-            self.cutoff_radius, True).compute(frame_generator)
+        self.nl = NeighborList(self.cutoff_radius, True, True).compute(frame_generator)
 
         pairwise_ellip_feat = pairwise_ellip_expansion(
             self.max_angular,
@@ -585,12 +580,9 @@ def transform(self, frames, show_progress=False, normalize=True, *, version: int
             version=version
         )
 
-        features = contract_pairwise_feat(
-            pairwise_ellip_feat, species, show_progress)
+        features = contract_pairwise_feat(pairwise_ellip_feat, species, show_progress)
 
         if normalize:
-            normalized_features = self.radial_basis.orthonormalize_basis(
-                features)
-            return normalized_features
+            return self.radial_basis.orthonormalize_basis(features)
         else:
             return features

tests/ex_input.py

@@ -62,7 +62,7 @@
 _comp_version = [1, _MOST_RECENT_VER]
 _test_files = [
     "ellipsoid_frames",
-    "ell-trimers"
+    # "ell-trimers"
     # "both_rotating_in_z", # Results in key error in frames.arrays['c_q']
     # "face_to_face",
     # "random_rotations",
@@ -348,8 +348,7 @@ def write_result_summary(file: TextIOWrapper, timer: SimpleTimer, err_dict: dict
         file.write(f"{err_dict.get(key):.4e}\n")
 
     file.write("\nNote: Number in parenthesis after runtime refers to corresponding runtime change compared to original implementation (version 0).\n")
-    file.write(
-        "      Negative runtime change means computation was faster compared to the original implementation.\n")
+    file.write("      Negative runtime change means computation was faster compared to the original implementation.\n")
 
 
 def write_raw_data(file: TextIOWrapper, raw_data: dict[str, list[list[float]]]):
@@ -364,10 +363,8 @@ def write_raw_data(file: TextIOWrapper, raw_data: dict[str, list[list[float]]]):
 
 
 if __name__ == "__main__":
-    actual_file_name = "comp_result_v" + \
-        ",".join([str(ver) for ver in _comp_version])
-    write_name = str(pathlib.Path(__file__).parent.absolute()) + \
-        "/time_results/" + actual_file_name + ".csv"
+    actual_file_name = "comp_result_v" + ",".join([str(ver) for ver in _comp_version])
+    write_name = str(pathlib.Path(__file__).parent.absolute()) + "/time_results/" + actual_file_name + ".csv"
     raw_results = dict()
     extra_infos = dict()
     errors = dict()
@@ -385,16 +382,14 @@ def write_raw_data(file: TextIOWrapper, raw_data: dict[str, list[list[float]]]):
 
         for ver in _comp_version:
             for test_file in _test_files:
-                file_path = str(pathlib.Path(__file__).parent.parent.absolute(
-                )) + "/benchmarks/two_particle_gb/" + test_file + ".xyz"
+                file_path = str(pathlib.Path(__file__).parent.parent.absolute()) + "/benchmarks/two_particle_gb/" + test_file + ".xyz"
 
                 for (param_index, (param, repeat_no)) in enumerate(_params):
                     iter_str = get_key(ver, param_index + 1, test_file)
 
                     for rep_index in tqdm(range(repeat_no), desc=f"{iter_str}"):
                         single_pass_timer.mark_start()
-                        comp_result, ex_info = single_pass(
-                            file_path, param, version=ver)
+                        comp_result, ex_info = single_pass(file_path, param, version=ver)
                         single_pass_timer.mark(iter_str)
 
                     # Only stores the result and extra info from the last iteration, as all iterations
@@ -403,8 +398,7 @@ def write_raw_data(file: TextIOWrapper, raw_data: dict[str, list[list[float]]]):
                     extra_infos.update({iter_str: ex_info})
 
                     # Get SSE based on the original implementation (v0) of equivalent parameter set and the test file
-                    errors.update({iter_str: total_error(
-                        raw_results.get(get_comp_key(iter_str)), comp_result)})
+                    errors.update({iter_str: total_error(raw_results.get(get_comp_key(iter_str)), comp_result)})
 
             # Make sure garbage collection does not interfere with the next iteration (version change).
             ClebschGordanReal.cache_list.clear_cache()

tests/time_results/comp_result_v0,1,2.csv

@@ -3,3 +3,38 @@ Comparison of versions [0 1 2]
 ---------------- Initialization Info ----------------
 initial_import time (sec),  0.0000
 
+----------------- Parameter Summary -----------------
+Parameter Set,l_max,sigma,r_cut,sigma_1,sigma_2,sigma_3,Rotation Quaternion
+p1,10,2.0,5.0,3.0,2.0,1.0,-0.7071 - 0.7071i + 0.0000j + 0.0000k
+p2,10,3.0,4.0,3.0,2.0,1.0,-0.7071 - 0.7071i + 0.0000j + 0.0000k
+p3,7,4.0,6.0,3.0,2.0,1.0,-0.7071 - 0.7071i + 0.0000j + 0.0000k
+p4,5,3.0,5.0,5.0,3.0,1.0,-0.7071 - 0.7071i + 0.0000j + 0.0000k
+p5,10,2.0,5.0,3.0,3.0,0.8,-0.7071 - 0.7071i + 0.0000j + 0.0000k
+p6,8,10.0,10.0,10.0,7.0,5.0,-0.7071 - 0.7071i + 0.0000j + 0.0000k
+
+------------------ Overall Summary ------------------
+Name,Maximum runtime (sec),Average runtime (sec),Median runtime (sec),SSE (from v0)
+v0_p1_ellipsoid_frames,3.1423 (0.00%),2.7798 (0.00%),2.9694 (0.00%),0.0000e+00
+v0_p2_ellipsoid_frames,6.3015 (0.00%),3.1810 (0.00%),2.4965 (0.00%),0.0000e+00
+v0_p3_ellipsoid_frames,1.2019 (0.00%),0.9835 (0.00%),0.9155 (0.00%),0.0000e+00
+v0_p4_ellipsoid_frames,0.5421 (0.00%),0.4584 (0.00%),0.4557 (0.00%),0.0000e+00
+v0_p5_ellipsoid_frames,4.3704 (0.00%),3.2551 (0.00%),3.0284 (0.00%),0.0000e+00
+v0_p6_ellipsoid_frames,1.8138 (0.00%),1.4145 (0.00%),1.3588 (0.00%),0.0000e+00
+
+v1_p1_ellipsoid_frames,2.2992 (-26.83%),0.5607 (-79.83%),0.3151 (-89.39%),5.6160e-31
+v1_p2_ellipsoid_frames,0.3154 (-95.00%),0.2812 (-91.16%),0.2741 (-89.02%),3.7748e-32
+v1_p3_ellipsoid_frames,0.4770 (-60.32%),0.2263 (-76.99%),0.1833 (-79.98%),0.0000e+00
+v1_p4_ellipsoid_frames,0.2562 (-52.73%),0.1531 (-66.60%),0.1365 (-70.05%),7.7037e-34
+v1_p5_ellipsoid_frames,0.3155 (-92.78%),0.2995 (-90.80%),0.2974 (-90.18%),6.9333e-33
+v1_p6_ellipsoid_frames,0.5709 (-68.53%),0.2688 (-81.00%),0.2205 (-83.77%),0.0000e+00
+
+v2_p1_ellipsoid_frames,1.4603 (-53.53%),0.4608 (-83.42%),0.3267 (-89.00%),5.6160e-31
+v2_p2_ellipsoid_frames,0.2883 (-95.42%),0.2729 (-91.42%),0.2699 (-89.19%),3.7748e-32
+v2_p3_ellipsoid_frames,0.5480 (-54.40%),0.2346 (-76.15%),0.1811 (-80.21%),0.0000e+00
+v2_p4_ellipsoid_frames,0.2527 (-53.38%),0.1467 (-68.00%),0.1294 (-71.61%),7.7037e-34
+v2_p5_ellipsoid_frames,0.3103 (-92.90%),0.2950 (-90.94%),0.2933 (-90.32%),6.9333e-33
+v2_p6_ellipsoid_frames,1.0280 (-43.32%),0.3344 (-76.36%),0.2294 (-83.12%),0.0000e+00
+
+Note: Number in parenthesis after runtime refers to corresponding runtime change compared to original implementation (version 0).
+      Negative runtime change means computation was faster compared to the original implementation.
+