remove the dependency of property num_atoms on the cube file content

remove the dependency of property num_atoms on the cube file content.
When writing a new cube file, the num_atoms property is obtained from
self.stc which is ase Atoms object

cp2kdata/cube/cube.py

@@ -1,23 +1,16 @@
-from cp2kdata.utils import file_content, interpolate_spline
-from cp2kdata.utils import au2A, au2eV
-from cp2kdata.cell import Cp2kCell
+import os
+from copy import deepcopy
+
 import numpy as np
 import matplotlib.pyplot as plt
-import os
 from scipy import fft
 from ase import Atom, Atoms
 from monty.json import MSONable
-from copy import deepcopy
 import asciichartpy as acp
 
-
-def square_wave_filter(x, l, cell_z):
-    half_l = l/2
-    x_1st, x_2nd = np.array_split(x, 2)
-    y_1st = np.heaviside(half_l - np.abs(x_1st), 0)/l
-    y_2nd = np.heaviside(half_l - np.abs(x_2nd-cell_z), 0)/l
-    y = np.concatenate([y_1st, y_2nd])
-    return y
+from cp2kdata.utils import file_content, interpolate_spline
+from cp2kdata.utils import au2A, au2eV
+from cp2kdata.cell import Cp2kCell
 
 # parse cp2kcube
 
@@ -119,11 +112,12 @@ def get_pav(self, axis="z", interpolate=False):
     def get_mav(self, l1, l2=0, ncov=1, interpolate=False):
         axis = "z"
         pav_x, pav = self.get_pav(axis=axis, interpolate=interpolate)
-        theta_1_fft = fft.fft(square_wave_filter(pav_x, l1, self.cell_z))
+        theta_1_fft = fft.fft(self.square_wave_filter(pav_x, l1, self.cell_z))
         pav_fft = fft.fft(pav)
         mav_fft = pav_fft*theta_1_fft*self.cell_z/len(pav_x)
         if ncov == 2:
-            theta_2_fft = fft.fft(square_wave_filter(pav_x, l2, self.cell_z))
+            theta_2_fft = fft.fft(
+                self.square_wave_filter(pav_x, l2, self.cell_z))
             mav_fft = mav_fft*theta_2_fft*self.cell_z/len(pav_x)
         mav = fft.ifft(mav_fft)
         return pav_x, np.real(mav)
@@ -137,14 +131,23 @@ def quick_plot(self, axis="z", interpolate=False, output_dir="./"):
         plt.legend()
         plt.savefig(os.path.join(output_dir, "pav.png"), dpi=100)
 
+    @staticmethod
+    def square_wave_filter(x, l, cell_z):
+        half_l = l/2
+        x_1st, x_2nd = np.array_split(x, 2)
+        y_1st = np.heaviside(half_l - np.abs(x_1st), 0)/l
+        y_2nd = np.heaviside(half_l - np.abs(x_2nd-cell_z), 0)/l
+        y = np.concatenate([y_1st, y_2nd])
+        return y
+
 
 class Cp2kCube(MSONable):
     # add MSONable use as_dict and from_dict
     """
     Documentation for the Cp2kCube class.
     """
 
-    def __init__(self, fname=None, cube_vals=None, cell=None, stc=None):
+    def __init__(self, fname: str = None, cube_vals: np.ndarray = None, cell: Cp2kCell = None, stc: Atoms = None):
         print("Warning: This is New Cp2kCube Class, if you want to use old Cp2kCube")
         print("try, from cp2kdata.cube.cube import Cp2kCubeOld")
         print("New Cp2kCube return raw values in cp2k cube file")
@@ -159,7 +162,7 @@ def __init__(self, fname=None, cube_vals=None, cell=None, stc=None):
         else:
             self.cell = cell
         if stc is None:
-            self.stc = self.get_stc()
+            self.stc = self._parse_stc()
         else:
             self.stc = stc
 
@@ -179,6 +182,12 @@ def read_cell(self):
 
     @property
     def num_atoms(self):
+        return len(self.stc)
+
+    def _parse_num_atoms(self):
+        """
+        be used to parse the number of atoms from the cube file only
+        """
         line = file_content(self.file, 2)
         num_atoms = int(line.split()[0])
         return num_atoms
@@ -215,9 +224,10 @@ def __sub__(self, others):
             raise RuntimeError("Unspported Class")
         return other_copy
 
-    def get_stc(self):
+    def _parse_stc(self):
+        num_atoms = self._parse_num_atoms()
         atom_list = []
-        for i in range(self.num_atoms):
+        for i in range(num_atoms):
             stc_vals = file_content(self.file, (6+i, 6+i+1))
             stc_vals = stc_vals.split()
             atom = Atom(
@@ -231,12 +241,14 @@ def get_stc(self):
         stc.set_cell(self.cell.cell_matrix*au2A)
         return stc
 
+    def get_stc(self):
+        return self.stc
+
     def copy(self):
         return deepcopy(self)
 
     def get_pav(self, axis='z', interpolate=False):
 
-
         # do the planar average along specific axis
         lengths = self.cell.get_cell_lengths()
         grid_point = self.cell.grid_point
@@ -247,7 +259,7 @@ def get_pav(self, axis='z', interpolate=False):
             length = lengths[0]
 
             np.testing.assert_array_equal(
-                self.cell.get_cell_angles()[[1,2]],
+                self.cell.get_cell_angles()[[1, 2]],
                 np.array([90.0, 90.0]),
                 err_msg=f"The axis x is not perpendicular to yz plane, the pav can not be used!"
             )
@@ -269,7 +281,7 @@ def get_pav(self, axis='z', interpolate=False):
             length = lengths[2]
 
             np.testing.assert_array_equal(
-                self.cell.get_cell_angles()[[0,1]],
+                self.cell.get_cell_angles()[[0, 1]],
                 np.array([90.0, 90.0]),
                 err_msg=f"The axis z is not perpendicular to xy plane, the pav can not be used!"
             )
@@ -297,11 +309,11 @@ def get_mav(self, l1, l2=0, ncov=1, interpolate=False, axis="z"):
         length = cell_length[axis]
 
         pav_x, pav = self.get_pav(axis=axis, interpolate=interpolate)
-        theta_1_fft = fft.fft(square_wave_filter(pav_x, l1, length))
+        theta_1_fft = fft.fft(self.square_wave_filter(pav_x, l1, length))
         pav_fft = fft.fft(pav)
         mav_fft = pav_fft*theta_1_fft*length/len(pav_x)
         if ncov == 2:
-            theta_2_fft = fft.fft(square_wave_filter(pav_x, l2, length))
+            theta_2_fft = fft.fft(self.square_wave_filter(pav_x, l2, length))
             mav_fft = mav_fft*theta_2_fft*length/len(pav_x)
         mav = fft.ifft(mav_fft)
         return pav_x, np.real(mav)
@@ -443,6 +455,15 @@ def read_cube_vals(fname, num_atoms, grid_point):
         cube_vals = cube_vals.reshape(grid_point)
         return cube_vals
 
+    @staticmethod
+    def square_wave_filter(x, l, cell_z):
+        half_l = l/2
+        x_1st, x_2nd = np.array_split(x, 2)
+        y_1st = np.heaviside(half_l - np.abs(x_1st), 0)/l
+        y_2nd = np.heaviside(half_l - np.abs(x_2nd-cell_z), 0)/l
+        y = np.concatenate([y_1st, y_2nd])
+        return y
+
 
 class Cp2kCubeTraj:
     def __init__(cube_dir, prefix):

tests/test_cube/test_cube.py

@@ -1,8 +1,10 @@
-from cp2kdata import Cp2kCube
 import os
+
 import pytest
 import numpy as np
 
+from cp2kdata import Cp2kCube
+
 
 path_prefix = "tests/test_cube/"
 cube_list = [Cp2kCube(os.path.join(path_prefix, "Si_bulk8-v_hartree-1_0.cube"))]