def test_matrix_2_abc(self):
'''Test the function for converting the lattice to abc, alpha,beta, gamma format'''
lattice = np.asarray([[2.715, 2.715, 0.], [0., 2.715, 2.715],
[2.715, 0., 2.715]])
a, b, c, a_vec, b_vec, c_vec = md.matrix_2_abc(lattice)
self.assertAlmostEqual(a, 3.8395898218429529)
self.assertAlmostEqual(b, 3.8395898218429529)
self.assertAlmostEqual(c, 3.8395898218429529)
"[WARNING] Fermi energy is not extracted. Shifting is not done\n"
)
print(
"[WARNING] fermi energy is not extracted. Shifting is not done"
)
else:
log.write("--------------------\n")
log.write("(Manually set) Fermi energy= [" + str(fermi_e) + " ] eV.\n")
log.write("--------------------\n")
#------------------------------------------------------------------
# Get the potential
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = md.read_vasp_density(input_file,
quiet=True)
vector_a, vector_b, vector_c, av, bv, cv = md.matrix_2_abc(Lattice)
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
grid_pot, electrons = md.density_2_grid(vasp_pot, NGX, NGY, NGZ)
#------------------------------------------------------------------
# POTENTIAL
#------------------------------------------------------------------
planar = md.planar_average(grid_pot, NGX, NGY, NGZ)
shifted_planar = planar - fermi_e
plt.plot(shifted_planar)
#------------start: MACROSCOPIC AVERAGE
if Macro_average:
macro = md.macroscopic_average(planar, lattice_vector, resolution_z)
import macrodensity as md
import math
import numpy as np
import matplotlib.pyplot as plt
import csv
from itertools import izip
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = md.read_vasp_density('LOCPOT.slab')
vector_a,vector_b,vector_c,av,bv,cv = md.matrix_2_abc(Lattice)
resolution_x = vector_a/NGX
resolution_y = vector_b/NGY
resolution_z = vector_c/NGZ
grid_pot, electrons = md.density_2_grid(vasp_pot,NGX,NGY,NGZ)
cutoff_varience = 1E-4
hanksConstant = 4.89E-7
## Get the gradiens (Field), if required.
## Comment out if not required, due to compuational expense.
#grad_x,grad_y,grad_z = np.gradient(grid_pot[:,:,:],resolution_x,resolution_y,resolution_z)
#------------------------------------------------------------------
##------------------------------------------------------------------
## Get the equation for the plane
## This is the section for plotting on a user defined plane;
import math
import numpy as np
import matplotlib.pyplot as plt
#------------------------------------------------------------------
# READING
# Get the two potentials and change them to a planar average.
# This section should not be altered
#------------------------------------------------------------------
# SLAB
vasp_pot, NGX, NGY, NGZ, Lattice = md.read_vasp_density('CHGCAR.Slab')
mag_a,mag_b,mag_c,vec_a,vec_b,vec_c = md.matrix_2_abc(Lattice)
resolution_x = mag_a/NGX
resolution_y = mag_b/NGY
resolution_z = mag_c/NGZ
Volume = md.get_volume(vec_a,vec_b,vec_c)
grid_pot_slab, electrons_slab = md.density_2_grid(vasp_pot,NGX,NGY,NGZ,True,Volume)
# Save the lattce vectors for use later
Vector_A = [vec_a,vec_b,vec_c]
#----------------------------------------------------------------------------------
# CONVERT TO PLANAR DENSITIES
#----------------------------------------------------------------------------------
planar_slab = md.planar_average(grid_pot_slab,NGX,NGY,NGZ)
# BULK
vasp_pot, NGX, NGY, NGZ, Lattice = md.read_vasp_density('CHGCAR.Bulk')
mag_a,mag_b,mag_c,vec_a,vec_b,vec_c = md.matrix_2_abc(Lattice)
resolution_x = mag_a/NGX
