Script to sum up the charge density around an atom

get_TotEle.py

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+#!/usr/bin/env python3
+
+'''
+#=====================================================
+# AUTHOR:  Asif Iqbal
+# GitHUB:  Asif_em
+# PURPOSE: Read CHGCAR file and compute the integrated
+#          charge density to sum up to # of electrons.
+#          Dependency on pymatgen module
+#          The following code is uploaded to my GitHub
+#          
+#=====================================================
+'''
+
+import numpy as np
+import matplotlib.pyplot as plt
+from pymatgen.io.vasp.outputs import VolumetricData
+
+poscar, data, data_aug = VolumetricData.parse_file('CHGCAR')
+latt = np.array(poscar.structure.lattice.matrix)
+
+# As per VASP the CHGCAR needs to be divided by Volume
+# COuld be total or diff if ISPIN = 2
+chgd = data["total"] / np.linalg.det(latt) 
+pos = poscar.structure.cart_coords
+# get volume per grid point
+dv = np.linalg.det(latt)/(np.array(chgd).shape[0]*np.array(chgd).shape[1]*np.array(chgd).shape[2])
+# get the step size in each direction (x, y, z)
+dr = latt/np.array(chgd).shape
+total_elect = np.sum(np.array(chgd))*dv
+num_grid_points = np.prod(np.array(chgd).shape)
+integrated_charge = np.cumsum(np.array(chgd)) * dv
+# Measure the charge density sphere
+distance = np.linspace(0, np.linalg.norm(dr), num_grid_points)
+
+print(dv, np.linalg.norm(dr))
+print(f"Shape of data in CHGCAR file:: {np.array(chgd).shape}")
+print(f"Total integrated electron number = {total_elect:8.5f}")
+# ploting 
+plt.plot(distance, integrated_charge, '-o', color='m', linewidth=0.5, markersize=0.5, markerfacecolor='none')
+plt.xlabel("Distance from the freestanding O atom (Å)")
+plt.ylabel("Integrated charge")
+plt.savefig('dvsQ.png', dpi=400, bbox_inches='tight')
+plt.show()
+