from gpaw.elf import ELF
# Graphene nanoribbon
ribbon = graphene_nanoribbon(5, 6, type='armchair', saturated=True, vacuum=3.5)
# Gold adsorbate
pos = (ribbon[35].position + ribbon[60].position) / 2.0
pos[1] += 2.2
adsorbate = Atoms('Au', (pos, ))
ribbon += adsorbate
ribbon.center(axis=1, vacuum=3.5)
txt = 'output_p_{}.txt'.format(size)
ribbon.calc = GPAW(
h=0.22,
xc='PBE',
txt=txt,
occupations=FermiDirac(0.2),
eigensolver=RMMDIIS(),
)
ribbon.get_potential_energy()
# Calculate electron localization function
elf = ELF(ribbon.calc)
elf.update()
elf_g = elf.get_electronic_localization_function(gridrefinement=2)
if rank == 0:
write('elf_ribbon.cube', ribbon, data=elf_g)
atoms = molecule("CO")
atoms.center(2.0)
txt = sys.stdout
txt = None
try:
atoms, calc = restart("CO.gpw", txt=txt)
energy = atoms.get_potential_energy()
except:
calc = GPAW(h=0.24, txt=txt)
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.write("CO.gpw", "all")
elf = ELF(calc)
elf.update()
elf_G = elf.get_electronic_localization_function(gridrefinement=1)
elf_g = elf.get_electronic_localization_function(gridrefinement=2)
nt_G = calc.density.nt_sG[0]
taut_G = elf.taut_sG[0]
nt_grad2_G = elf.nt_grad2_sG[0]
nt_grad2_g = elf.nt_grad2_sg[0]
# integrate the CO bond
if rank == 0:
# bond area
x0 = (atoms.positions[0][0] - 1.0) / atoms.get_cell()[0, 0]
x1 = 1 - x0
y0 = (atoms.positions[0][1] - 1.0) / atoms.get_cell()[1, 1]
from ase.data.molecules import molecule
from gpaw import GPAW
from gpaw.elf import ELF
from gpaw.test import equal
from gpaw.mpi import rank
atoms = molecule('CO')
atoms.center(2.0)
calc = GPAW(h=0.24)
atoms.set_calculator(calc)
atoms.get_potential_energy()
elf = ELF(calc)
elf.initialize(calc)
elf.update(calc.wfs)
elf_G = elf.get_electronic_localization_function(spin=0, gridrefinement=1)
elf_g = elf.get_electronic_localization_function(spin=0, gridrefinement=2)
# integrate the CO bond
if rank == 0:
# bond area
x0 = (atoms.positions[0][0] - 1.0) / atoms.get_cell()[0, 0]
x1 = 1 - x0
y0 = (atoms.positions[0][1] - 1.0) / atoms.get_cell()[1, 1]
y1 = 1 - y0
z0 = atoms.positions[1][2] / atoms.get_cell()[2, 2]
z1 = atoms.positions[0][2] / atoms.get_cell()[2, 2]
gd = calc.wfs.gd
Gx0, Gx1 = gd.N_c[0] * x0, gd.N_c[0] * x1
Gy0, Gy1 = gd.N_c[1] * y0, gd.N_c[1] * y1
Gz0, Gz1 = gd.N_c[2] * z0, gd.N_c[2] * z1
finegd = calc.density.finegd
import sys from gpaw import GPAW from gpaw import restart from ase.io import write from gpaw.elf import ELF filename = sys.argv[1] atoms, calc = restart(filename) calc.set_positions() elf = ELF(calc) #elf.initialize(calc) #elf.update(calc.wfs) elf.update() elf_out = elf.get_electronic_localization_function(gridrefinement=2) ## Write to file ## write(filename+'.plt', atoms, data=elf_out) write(filename + '.cube', atoms, data=elf_out)
atoms = molecule('CO')
atoms.center(2.0)
txt = sys.stdout
txt = None
try:
atoms, calc = restart('CO.gpw', txt=txt)
energy = atoms.get_potential_energy()
except:
calc = GPAW(h=0.24, txt=txt)
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.write('CO.gpw', 'all')
elf = ELF(calc)
elf.update()
elf_G = elf.get_electronic_localization_function(gridrefinement=1)
elf_g = elf.get_electronic_localization_function(gridrefinement=2)
nt_G = calc.density.nt_sG[0]
taut_G = elf.taut_sG[0]
nt_grad2_G = elf.nt_grad2_sG[0]
nt_grad2_g = elf.nt_grad2_sg[0]
# integrate the CO bond
if rank == 0:
# bond area
x0 = (atoms.positions[0][0] - 1.0) / atoms.get_cell()[0, 0]
x1 = 1 - x0
y0 = (atoms.positions[0][1] - 1.0) / atoms.get_cell()[1, 1]
from ase.data.molecules import molecule
from gpaw import GPAW
from gpaw.elf import ELF
from gpaw.test import equal
from gpaw.mpi import rank
atoms = molecule('CO')
atoms.center(2.0)
calc = GPAW(h=0.24)
atoms.set_calculator(calc)
atoms.get_potential_energy()
elf = ELF(calc)
elf.initialize(calc)
elf.update(calc.wfs)
elf_G = elf.get_electronic_localization_function(spin=0,gridrefinement=1)
elf_g = elf.get_electronic_localization_function(spin=0,gridrefinement=2)
# integrate the CO bond
if rank == 0:
# bond area
x0 = (atoms.positions[0][0] - 1.0)/atoms.get_cell()[0,0]
x1 = 1 - x0
y0 = (atoms.positions[0][1] -1.0)/atoms.get_cell()[1,1]
y1 = 1 - y0
z0 = atoms.positions[1][2]/atoms.get_cell()[2,2]
z1 = atoms.positions[0][2]/atoms.get_cell()[2,2]
gd = calc.wfs.gd
Gx0, Gx1 = gd.N_c[0]*x0, gd.N_c[0] * x1
Gy0, Gy1 = gd.N_c[1]*y0, gd.N_c[1] * y1
Gz0, Gz1 = gd.N_c[2]*z0, gd.N_c[2] * z1
finegd = calc.density.finegd
