#! /usr/bin/env python
import NewPotentialModule as pot
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 = pot.read_vasp_density('LOCPOT.slab')
vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a/NGX
resolution_y = vector_b/NGY
resolution_z = vector_c/NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ)
## 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;
## uncomment commands if this is the option that you want.
import csv
from itertools import izip
potential_file = 'LOCPOT' # The file with VASP output for potential
coordinate_file = 'POSCAR' # The coordinates file NOTE NOTE This must be in vasp 4 format
species = "O" # The species whose on-site potential you are interested in
sample_cube = [
5, 5, 5
] # The size of the sampling cube in units of mesh points (NGX/Y/Z)
# Nothing below here should require changing
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(potential_file)
vector_a, vector_b, vector_c, av, bv, cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot, NGX, NGY, NGZ)
## 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)
#------------------------------------------------------------------
##------------------------------------------------------------------
## Getting the potentials for a group of atoms, in this case the Os
## NOTE THIS REQUIRES ASE to be available https://wiki.fysik.dtu.dk/ase/index.html
##------------------------------------------------------------------
import numpy as np import matplotlib.pyplot as plt ## Input section (define the plane with 3 points, fractional coordinates) a_point = [0, 0, 0] b_point = [1, 0, 1] c_point = [0, 1, 0] input_file = 'LOCPOT.slab' #------------------------------------------------------------------ # Get the potential # This section should not be altered #------------------------------------------------------------------ vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(input_file) vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice) resolution_x = vector_a/NGX resolution_y = vector_b/NGY resolution_z = vector_c/NGZ grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ) ## 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; ## uncomment commands if this is the option that you want.
#! /usr/bin/env python
import NewPotentialModule as pot
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 = pot.read_vasp_density('LOCPOT.slab')
vector_a, vector_b, vector_c, av, bv, cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot, NGX, NGY, NGZ)
## 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;
## uncomment commands if this is the option that you want.
##------------------------------------------------------------------
## Input section (define the plane with 3 points)
#a_point = [0, 0, 0]
# This section should not be altered
#------------------------------------------------------------------
#vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(input_file)
#vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice)
#resolution_x = vector_a/NGX
#resolution_y = vector_b/NGY
#resolution_z = vector_c/NGZ
#grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ)
potential, atoms = ase.io.cube.read_cube(input_file, read_data=True)
vector_a = np.linalg.norm(atoms.cell[1])
vector_b = np.linalg.norm(atoms.cell[1])
vector_c = np.linalg.norm(atoms.cell[2])
NGX = len(potential)
NGY = len(potential[0])
NGZ = len(potential[0][0])
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
print NGX, NGY, NGZ
#------------------------------------------------------------------
## POTENTIAL
planar = pot.planar_average(potential, NGX, NGY, NGZ)
## MACROSCOPIC AVERAGE
macro = pot.macroscopic_average(planar, lattice_vector, resolution_z)
plt.plot(planar)
plt.plot(macro)
plt.savefig('Planar.eps')
#plt.show()
np.savetxt(output_file, planar)
##------------------------------------------------------------------
#! /usr/bin/env python
import NewPotentialModule as pot
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 = pot.read_vasp_density('LOCPOT.slab')
vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a/NGX
resolution_y = vector_b/NGY
resolution_z = vector_c/NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ)
## 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;
## uncomment commands if this is the option that you want.
import NewPotentialModule as pot
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 = pot.read_vasp_density('CHGCAR.Slab')
mag_a,mag_b,mag_c,vec_a,vec_b,vec_c = pot.matrix_2_abc(Lattice)
resolution_x = mag_a/NGX
resolution_y = mag_b/NGY
resolution_z = mag_c/NGZ
Volume = pot.get_volume(vec_a,vec_b,vec_c)
grid_pot_slab, electrons_slab = pot.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 = pot.planar_average(grid_pot_slab,NGX,NGY,NGZ)
# BULK
vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density('CHGCAR.Bulk')
mag_a,mag_b,mag_c,vec_a,vec_b,vec_c = pot.matrix_2_abc(Lattice)
#! /usr/bin/env python
import NewPotentialModule as pot
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 = pot.read_vasp_density('LOCPOT.slab')
vector_a, vector_b, vector_c, av, bv, cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot, NGX, NGY, NGZ)
## 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;
## uncomment commands if this is the option that you want.
##------------------------------------------------------------------
## Input section (define the plane with 3 points)
#a_point = [0, 0, 0]
#b_point = [1, 0, 1]
import matplotlib.pyplot as plt import csv from itertools import izip potential_file = 'LOCPOT' # The file with VASP output for potential coordinate_file = 'POSCAR' # The coordinates file NOTE NOTE This must be in vasp 4 format species = "O" # The species whose on-site potential you are interested in sample_cube = [5,5,5] # The size of the sampling cube in units of mesh points (NGX/Y/Z) # Nothing below here should require changing #------------------------------------------------------------------ # Get the potential # This section should not be altered #------------------------------------------------------------------ vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(potential_file) vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice) resolution_x = vector_a/NGX resolution_y = vector_b/NGY resolution_z = vector_c/NGZ grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ) ## 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) #------------------------------------------------------------------ ##------------------------------------------------------------------ ## Getting the potentials for a group of atoms, in this case the Os ## NOTE THIS REQUIRES ASE to be available https://wiki.fysik.dtu.dk/ase/index.html ##------------------------------------------------------------------ ##------------------------------------------------------------------
import math
import numpy as np
import matplotlib.pyplot as plt
## Input section (define the plane with 3 points, fractional coordinates)
a_point = [0, 0, 0]
b_point = [1, 0, 1]
c_point = [0, 1, 0]
input_file = 'LOCPOT.slab'
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(input_file)
vector_a, vector_b, vector_c, av, bv, cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot, NGX, NGY, NGZ)
## 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;
## uncomment commands if this is the option that you want.
#! /usr/bin/env python
import NewPotentialModule as pot
import math
import numpy as np
import matplotlib.pyplot as plt
input_file = 'LOCPOT'
lattice_vector = 4.75
output_file = 'planar.dat'
# No need to alter anything after here
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(input_file)
vector_a, vector_b, vector_c, av, bv, cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a / NGX
resolution_y = vector_b / NGY
resolution_z = vector_c / NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot, NGX, NGY, NGZ)
#------------------------------------------------------------------
## POTENTIAL
planar = pot.planar_average(grid_pot, NGX, NGY, NGZ)
## MACROSCOPIC AVERAGE
macro = pot.macroscopic_average(planar, lattice_vector, resolution_z)
plt.plot(planar)
plt.plot(macro)
plt.savefig('Planar.eps')
plt.show()
np.savetxt(output_file, planar)
##------------------------------------------------------------------
#! /usr/bin/env python
import NewPotentialModule as pot
import math
import numpy as np
import matplotlib.pyplot as plt
input_file = 'LOCPOT'
lattice_vector = 4.75
output_file = 'planar.dat'
# No need to alter anything after here
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(input_file)
vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice)
resolution_x = vector_a/NGX
resolution_y = vector_b/NGY
resolution_z = vector_c/NGZ
grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ)
#------------------------------------------------------------------
## POTENTIAL
planar = pot.planar_average(grid_pot,NGX,NGY,NGZ)
## MACROSCOPIC AVERAGE
macro = pot.macroscopic_average(planar,lattice_vector,resolution_z)
plt.plot(planar)
plt.plot(macro)
plt.savefig('Planar.eps')
plt.show()
np.savetxt(output_file,planar)
##------------------------------------------------------------------
# This section should not be altered
#------------------------------------------------------------------
#vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density(input_file)
#vector_a,vector_b,vector_c,av,bv,cv = pot.matrix_2_abc(Lattice)
#resolution_x = vector_a/NGX
#resolution_y = vector_b/NGY
#resolution_z = vector_c/NGZ
#grid_pot, electrons = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ)
potential, atoms = ase.io.cube.read_cube(input_file,read_data=True)
vector_a = np.linalg.norm(atoms.cell[1])
vector_b = np.linalg.norm(atoms.cell[1])
vector_c = np.linalg.norm(atoms.cell[2])
NGX = len(potential)
NGY = len(potential[0])
NGZ = len(potential[0][0])
resolution_x = vector_a/NGX
resolution_y = vector_b/NGY
resolution_z = vector_c/NGZ
print NGX,NGY,NGZ
#------------------------------------------------------------------
## POTENTIAL
planar = pot.planar_average(potential,NGX,NGY,NGZ)
## MACROSCOPIC AVERAGE
macro = pot.macroscopic_average(planar,lattice_vector,resolution_z)
plt.plot(planar)
plt.plot(macro)
plt.savefig('Planar.eps')
#plt.show()
np.savetxt(output_file,planar)
##------------------------------------------------------------------
import NewPotentialModule as pot
import math
import numpy as np
import matplotlib.pyplot as plt
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#------------------------------------------------------------------
vasp_pot, NGX, NGY, NGZ, Lattice = pot.read_vasp_density('LOCPOT')
vector_a,vector_b,vector_c = pot.matrix_2_abc(Lattice)
resolution_x = vector_a/NGX
resolution_y = vector_b/NGY
resolution_z = vector_c/NGZ
grid_pot = pot.density_2_grid(vasp_pot,NGX,NGY,NGZ)
## 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;
## uncomment commands if this is the option that you want.
##------------------------------------------------------------------
