removed unused variables and cleaned up imports

Author: wladerer

test/test_wavecar.py

@@ -1,5 +1,4 @@
 import argparse
-from typing import Union
 
 
 def is_number(s):

vsh/scripts/__init__.py

@@ -3,7 +3,7 @@
 from ase.calculators.vasp import Vasp
 from ase.spacegroup import get_spacegroup
 from ase import Atoms
-from ase.io import read, write
+from ase.io import read
 from scipy.spatial.distance import cdist
 import numpy as np
 
@@ -18,7 +18,7 @@ def validate_atoms(atoms: Atoms) -> bool:
 
 def is_diatomic(atoms: Atoms) -> bool:
     """Checks if an atoms object is diatomic"""
-    if validate_atoms(atoms) == False:
+    if validate_atoms(atoms) is False:
         raise ValueError("Invalid atoms object")
     if len(atoms) == 2:
         return True
@@ -28,7 +28,7 @@ def is_diatomic(atoms: Atoms) -> bool:
 
 def get_adjacency_matrix(atoms: Atoms) -> np.ndarray:
     """Gets the adjacency matrix of a structure"""
-    if validate_atoms(atoms) == False:
+    if validate_atoms(atoms) is False:
         raise ValueError("Invalid atoms object")
     # get the positions of the atoms object
     positions = atoms.get_positions()
@@ -93,7 +93,7 @@ def conflicting_atoms(atoms: Atoms, min_dist: float) -> dict:
     indices, bond_lengths = analyze_adjacency_matrix(neighbor_list, min_dist)
     element_list: tuple[np.ndarray] = atoms.get_chemical_symbols()
 
-    if indices == None or len(indices) == 0:
+    if indices is None or len(indices) == 0:
         return None
 
     print(indices)
@@ -107,7 +107,7 @@ def conflicting_atoms(atoms: Atoms, min_dist: float) -> dict:
 
 def print_conflicts(conflicts: dict):
     """Prints the conflicting atoms"""
-    if conflicts == None:
+    if conflicts is None:
         print("No conflicting atoms")
     else:
         print("Atom pair Bond length")
@@ -119,7 +119,6 @@ def print_conflicts(conflicts: dict):
 
 def check_convergence(file: str = "./vasprun.xml") -> list[bool]:
     """Looks for vasprun.xml file and checks if converged"""
-    import os
 
     # import Vasprun from pymatgen
     from pymatgen.io.vasp.outputs import Vasprun
@@ -211,7 +210,6 @@ def get_converged(args):
 
 def get_equivalent_positions(pmg_structure):
     """Get the equivalent positions of a structure"""
-    from pymatgen.core.structure import Structure
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
     spacegroup = SpacegroupAnalyzer(pmg_structure)

vsh/scripts/analysis.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from ase.io import read, write
+from ase.io import read
 import pyprocar
 
 orbital_dict = {
@@ -110,7 +110,6 @@ def plot_procar(args):
 
 def filter_procar(args):
     """Filters procar file based on user input"""
-    from pymatgen.io.vasp.outputs import Procar
 
     pyprocar.filter(args.input, args.output, bands=[584, 652])
 

vsh/scripts/band.py

@@ -4,7 +4,6 @@
 import matplotlib.pyplot as plt
 import pandas as pd
 import networkx as nx
-from mpl_toolkits import axes_grid1
 
 
 plt.style.use("seaborn-v0_8-colorblind")
@@ -154,7 +153,7 @@ def plot_icohp_graph(args):
         edges = G.edges()
         weights = [G[u][v]["ICOHP"] for u, v in edges]
         nx.draw(G, pos, edge_color=weights, width=2, edge_cmap=plt.cm.plasma)
-        pathcollection = nx.draw_networkx_nodes(
+        nx.draw_networkx_nodes(
             G, pos, node_size=600, node_color="black"
         )
         nx.draw_networkx_labels(

vsh/scripts/cohp.py

@@ -1,4 +1,4 @@
-from ase.io import read, write
+from ase.io import read
 import numpy as np
 
 two_d_kpath_template = """Two dimensional Kpath 

vsh/scripts/kpoints.py

@@ -4,12 +4,10 @@
 from PIL import Image
 import os
 
+from pymatgen.io.vasp import Poscar, Incar, Kpoints
 
 def validate_input(args):
     """Validates that INCAR, POSCAR, KPOINTS, and POTCAR files are present and formatted correctly"""
-    from pymatgen.io.vasp import Incar, Poscar, Kpoints, Potcar
-    import os
-
     # check that each file exists
     directory = args.input
     incar_file = os.path.join(directory, "INCAR")
@@ -173,7 +171,6 @@ def write_data_pickle(args):
 
 def unpack_pickle(args):
     """Unpacks POSCAR, INCAR, CONTCAR, and KPOINTS from a pickle file"""
-    from pymatgen.io.vasp import Poscar, Incar, Kpoints
     import pandas as pd
 
     try:
@@ -228,7 +225,7 @@ def unpack_pickle(args):
 
 def reconstitute_vasprun(file: str):
     """Unpacks POSCAR, INCAR, CONTCAR, and KPOINTS from a vasprun.xml file"""
-    from pymatgen.io.vasp import Vasprun, Poscar, Incar, Kpoints
+    from pymatgen.io.vasp import Vasprun
 
     # Load the vasprun file
     vasprun = Vasprun(
@@ -249,7 +246,6 @@ def reconstitute_vasprun(file: str):
 
 def unpack_vasprun(args):
     """Unpacks POSCAR, INCAR, CONTCAR, and KPOINTS from a vasprun.xml file"""
-    from pymatgen.io.vasp import Poscar, Incar, Kpoints
 
     poscar, incar, kpoints, contcar = reconstitute_vasprun(args.input)
 

vsh/scripts/manage.py

@@ -1,4 +1,4 @@
-from ase.io import read, write
+from ase.io import read
 from pymatgen.io.vasp.inputs import Poscar, Potcar
 
 

vsh/scripts/potcar.py

@@ -335,7 +335,7 @@ def plot_kpoint_orbital_variation(args):
             x=kpoints,
             y=sum_values,
             mode="lines",
-            name=f"Charge Spilling",
+            name="Charge Spilling",
             line=dict(color="grey", dash="dash", width=1),
         )
     )
@@ -458,7 +458,6 @@ def plot_compositional_variation(args):
 
 def analyze_kpoint(args):
     """Summarizes the data for a specific kpoint"""
-    dataframe = load_dataframe_from_file(args.input)
     kpoint = args.kpoint
     band = args.band
 

vsh/scripts/procar.py

@@ -3,7 +3,6 @@
 from pymatgen.io.vasp.outputs import Vasprun
 import pickle
 import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
 
 
 def projected_eigenvalues_from_pickle(file: str) -> pd.DataFrame:

vsh/utils/fermi_surface.py

@@ -1,7 +1,5 @@
 from vsh.scripts.procar import load_dataframe_from_file, add_kpoint_labels
 from pymatgen.io.vasp import Vasprun
-from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from pymatgen.core.structure import Structure
 
 
 # get ions from vasprun
@@ -58,7 +56,6 @@ def plot_compositional_variation(file: str, band: int, labels: list[str] = None)
 
 def get_equivalent_positions(pmg_structure):
     """Get the equivalent positions of a structure"""
-    from pymatgen.core.structure import Structure
     from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
 
     spacegroup = SpacegroupAnalyzer(pmg_structure)

vsh/utils/procar_tools.py

@@ -1,6 +1,5 @@
 import numpy as np
 from matplotlib import pyplot as plt
-import matplotlib.font_manager as fm
 
 
 def get_plot_stm_from_dat(file: str, gridsize: int = 300) -> plt:

vsh/utils/stm_tools.py

@@ -147,7 +147,6 @@ def plot_atomic_drift(initial_file: str, final_file: str, output_file: str = Non
     """Plots the atomic drift between two structures"""
     import sisl
     import sisl.viz
-    import numpy as np
 
     intial_atoms = read(initial_file)
     final_atoms = read(final_file)