vdos._set_efermi(efermi)
e = vdos.energy
dos_up = vdos.dos[0]
dos_down = vdos.dos[1]
dos_total = dos_up + dos_down
dos_s_up = np.zeros(len(e))
dos_p_up = np.zeros(len(e))
dos_d_up = np.zeros(len(e))
dos_s_down = np.zeros(len(e))
dos_p_down = np.zeros(len(e))
dos_d_down = np.zeros(len(e))
for i in range(len(atoms)):
dos_s_up += vdos.site_dos(i, 's-up')
dos_p_up += vdos.site_dos(i, 'px-up') + vdos.site_dos(
i, 'py-up') + vdos.site_dos(i, 'pz-up')
dos_d_up += vdos.site_dos(i, 'dxy-up') + vdos.site_dos(
i, 'dyz-up') + vdos.site_dos(i, 'dz2-up') + vdos.site_dos(
i, 'dxz-up') + vdos.site_dos(i, 'dx2-up')
dos_s_down += vdos.site_dos(i, 's-down')
dos_p_down += vdos.site_dos(i, 'px-down') + vdos.site_dos(
i, 'py-down') + vdos.site_dos(i, 'pz-down')
dos_d_down += vdos.site_dos(i, 'dxy-down') + vdos.site_dos(
i, 'dyz-down') + vdos.site_dos(i, 'dz2-down') + vdos.site_dos(
i, 'dxz-down') + vdos.site_dos(i, 'dx2-down')
#dos_s_up = vdos.site_dos(4,'s-up')
#dos_p_up = vdos.site_dos(4,'px-up') + vdos.site_dos(4,'py-up') + vdos.site_dos(4, 'pz-up')
bulk = Atoms([Atom('Pd', (0.0, 0.0, 0.0))],
cell=[(0, b, b), (b, 0, b), (b, b, 0)])
with jasp(
'bulk/pd-ados',
encut=300,
xc='PBE',
lreal=False,
rwigs=[1.5], # wigner-seitz radii for ados
kpts=(8, 8, 8),
atoms=bulk) as calc:
# this runs the calculation
bulk.get_potential_energy()
# now get results
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy # energy is an attribute, not a function
dos = ados.site_dos(0, 'd') # this is a function, get d-orbitals on atom 0
# we will select energies in the range of -10, 5
ind = (energies < 5) & (energies > -10)
energies = energies[ind]
dos = dos[ind]
Nstates = np.trapz(dos, energies)
occupied = energies <= 0.0
N_occupied_states = np.trapz(dos[occupied], energies[occupied])
# first moment
ed = np.trapz(energies * dos, energies) / Nstates
# second moment
wd2 = np.trapz(energies**2 * dos, energies) / Nstates
print 'Total # states = {0:1.2f}'.format(Nstates)
print 'number of occupied states = {0:1.2f}'.format(N_occupied_states)
print 'd-band center = {0:1.2f} eV'.format(ed)
print 'd-band width = {0:1.2f} eV'.format(np.sqrt(wd2))
cell=[(0, b, b),
(b, 0, b),
(b, b, 0)])
with jasp('bulk/pd-ados',
encut=300,
xc='PBE',
lreal=False,
rwigs=[1.5], # wigner-seitz radii for ados
kpts=(8, 8, 8),
atoms=bulk) as calc:
# this runs the calculation
bulk.get_potential_energy()
# now get results
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy # energy is an attribute, not a function
dos = ados.site_dos(0, 'd') # this is a function, get d-orbitals on atom 0
# we will select energies in the range of -10, 5
ind = (energies < 5) & (energies > -10)
energies = energies[ind]
dos = dos[ind]
Nstates = np.trapz(dos, energies)
occupied = energies <= 0.0
N_occupied_states = np.trapz(dos[occupied], energies[occupied])
# first moment
ed = np.trapz(energies * dos, energies) / Nstates
# second moment
wd2 = np.trapz(energies**2 * dos, energies) / Nstates
print 'Total # states = {0:1.2f}'.format(Nstates)
print 'number of occupied states = {0:1.2f}'.format(N_occupied_states)
print 'd-band center = {0:1.2f} eV'.format(ed)
print 'd-band width = {0:1.2f} eV'.format(np.sqrt(wd2))
vdos._set_efermi(efermi)
e = vdos.energy
dos_up = vdos.dos[0]
dos_down = vdos.dos[1]
dos_total = dos_up + dos_down
dos_s_up = np.zeros(len(e))
dos_p_up = np.zeros(len(e))
dos_d_up = np.zeros(len(e))
dos_s_down = np.zeros(len(e))
dos_p_down = np.zeros(len(e))
dos_d_down = np.zeros(len(e))
for i in range(len(atoms)):
dos_s_up += vdos.site_dos(i,'s-up')
dos_p_up += vdos.site_dos(i,'px-up') + vdos.site_dos(i,'py-up') + vdos.site_dos(i,'pz-up')
dos_d_up += vdos.site_dos(i,'dxy-up') + vdos.site_dos(i,'dyz-up') + vdos.site_dos(i,'dz2-up') + vdos.site_dos(i,'dxz-up') + vdos.site_dos(i,'dx2-up')
dos_s_down += vdos.site_dos(i, 's-down')
dos_p_down += vdos.site_dos(i, 'px-down') + vdos.site_dos(i, 'py-down') + vdos.site_dos(i, 'pz-down')
dos_d_down += vdos.site_dos(i, 'dxy-down') + vdos.site_dos(i, 'dyz-down') + vdos.site_dos(i, 'dz2-down') + vdos.site_dos(i,'dxz-down') + vdos.site_dos(i,'dx2-down')
#dos_s_up = vdos.site_dos(4,'s-up')
#dos_p_up = vdos.site_dos(4,'px-up') + vdos.site_dos(4,'py-up') + vdos.site_dos(4, 'pz-up')
#dos_s_down = vdos.site_dos(0,'s-down')
#dos_p_down = vdos.site_dos(0,'px-down') + vdos.site_dos(0,'py-down') + vdos.site_dos(0,'pz-down')
#dos_d_down = vdos.site_dos(0,'dxy-down') + vdos.site_dos(0,'dyz-down') + vdos.site_dos(0,'dz2-down') + vdos.site_dos(0,'dxz-down') + vdos.site_dos(0,'dx2-down')
plt.plot([-10,10],[0,0],color='black')
plt.plot(e, dos_total, label='total', color='b')
def calc_to_dict(calc, **kwargs):
d = {'doc': '''JSON representation of a VASP calculation.
energy is in eV
forces are in eV/\AA
stress is in GPa (sxx, syy, szz, syz, sxz, sxy)
magnetic moments are in Bohr-magneton
The density of states is reported with E_f at 0 eV.
Volume is reported in \AA^3
Coordinates and cell parameters are reported in \AA
If atom-projected dos are included they are in the form:
{ados:{energy:data, {atom index: {orbital : dos}}}
'''}
d['incar'] = {'doc': 'INCAR parameters'}
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.float_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.exp_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.string_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.int_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.bool_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.list_params.items())))
d['incar'].update(dict(filter(lambda item: item[1] is not None,
calc.dict_params.items())))
d['input'] = calc.input_params
d['potcar'] = calc.get_pseudopotentials()
d['atoms'] = atoms_to_dict(calc.get_atoms())
d['data'] = {'doc': 'Data from the output of the calculation'}
atoms = calc.get_atoms()
d['data']['total_energy'] = atoms.get_potential_energy()
d['data']['forces'] = atoms.get_forces().tolist()
# There are times when no stress is calculated
try:
stress = atoms.get_stress()
except NotImplementedError:
stress = None
except AssertionError:
stress = None
if stress is not None:
d['data']['stress'] = atoms.get_stress().tolist()
else:
d['data']['stress'] = None
d['data']['fermi_level'] = calc.get_fermi_level()
d['data']['volume'] = atoms.get_volume()
if calc.spinpol:
d['data']['magmom'] = atoms.get_magnetic_moment()
if (calc.int_params.get('lorbit', 0) >= 10
or calc.list_params.get('rwigs', None)):
try:
d['data']['magmoms'] = atoms.get_magnetic_moments().tolist()
except AttributeError:
d['data']['magmoms'] = None
# store the metadata
if hasattr(calc, 'metadata'):
d['metadata'] = calc.metadata
if kwargs.get('dos', None):
from ase.dft.dos import DOS
dos = DOS(calc, width=kwargs.get('width', 0.2))
e = dos.get_energies()
d['data']['dos'] = {'doc': 'Total density of states'}
d['data']['dos']['e'] = e.tolist()
if calc.spinpol:
d['data']['dos']['dos-up'] = dos.get_dos(spin=0).tolist()
d['data']['dos']['dos-down'] = dos.get_dos(spin=1).tolist()
else:
d['data']['dos']['dos'] = dos.get_dos().tolist()
if kwargs.get('ados', None):
from ase.calculators.vasp import VaspDos
ados = VaspDos(efermi=calc.get_fermi_level())
d['data']['ados'] = {'doc': 'Atom projected DOS'}
nonspin_orbitals_no_phase = ['s', 'p', 'd']
nonspin_orbitals_phase = ['s', 'py', 'pz', 'px',
'dxy', 'dyz', 'dz2', 'dxz', 'dx2']
spin_orbitals_no_phase = []
for x in nonspin_orbitals_no_phase:
spin_orbitals_no_phase += ['{0}-up'.format(x)]
spin_orbitals_no_phase += ['{0}-down'.format(x)]
spin_orbitals_phase = []
for x in nonspin_orbitals_phase:
spin_orbitals_phase += ['{0}-up'.format(x)]
spin_orbitals_phase += ['{0}-down'.format(x)]
if calc.spinpol and calc.int_params['lorbit'] != 11:
orbitals = spin_orbitals_no_phase
elif calc.spinpol and calc.int_params['lorbit'] == 11:
orbitals = spin_orbitals_phase
elif calc.int_params['lorbit'] != 11:
orbitals = nonspin_orbitals_no_phase
else:
orbitals = nonspin_orbitals_phase
for i, atom in enumerate(atoms):
d['data']['ados']['energy'] = ados.energy.tolist()
d['data']['ados'][i] = {}
for orbital in orbitals:
d['data']['ados'][i][orbital] = ados.site_dos(0, orbital).tolist()
# convert all numpy arrays to lists
for key in d:
try:
d[key] = d[key].tolist()
except:
pass
for key in d['input']:
try:
d['input'][key] = d['input'][key].tolist()
except:
pass
return d
(b, b, 0)])
RWIGS = [1.0, 1.1, 1.25, 1.5, 2.0, 2.5, 3.0, 4.0, 5.0 ]
ED, WD, N = [], [], []
for rwigs in RWIGS:
with jasp('bulk/pd-ados') as calc:
calc.clone('bulk/pd-ados-rwigs-{0}'.format(rwigs))
with jasp('bulk/pd-ados-rwigs-{0}'.format(rwigs)) as calc:
calc.set(rwigs=[rwigs])
try:
calc.calculate()
except (VaspSubmitted, VaspQueued):
continue
# now get results
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy
dos = ados.site_dos(0, 'd')
#we will select energies in the range of -10, 5
ind = (energies < 5) & (energies > -10)
energies = energies[ind]
dos = dos[ind]
Nstates = np.trapz(dos, energies)
occupied = energies <= 0.0
N_occupied_states = np.trapz(dos[occupied], energies[occupied])
ed = np.trapz(energies * dos, energies) / np.trapz(dos, energies)
wd2 = np.trapz(energies**2 * dos, energies) / np.trapz(dos, energies)
N.append(N_occupied_states)
ED.append(ed)
WD.append(wd2**0.5)
plt.plot(RWIGS, N, 'bo', label='N. occupied states')
plt.legend(loc='best')
plt.xlabel('RWIGS ($\AA$)')
def calc_to_dict(calc, **kwargs):
"""Convert calc to a dictionary."""
d = {
'doc':
'''JSON representation of a VASP calculation.
energy is in eV
forces are in eV/\AA
stress is in GPa (sxx, syy, szz, syz, sxz, sxy)
magnetic moments are in Bohr-magneton
The density of states is reported with E_f at 0 eV.
Volume is reported in \AA^3
Coordinates and cell parameters are reported in \AA
If atom-projected dos are included they are in the form:
{ados:{energy:data, {atom index: {orbital : dos}}}
'''
}
d['incar'] = {'doc': 'INCAR parameters'}
d['incar'].update(
dict(
filter(lambda item: item[1] is not None,
calc.float_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.exp_params.items())))
d['incar'].update(
dict(
filter(lambda item: item[1] is not None,
calc.string_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.int_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.bool_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.list_params.items())))
d['incar'].update(
dict(filter(lambda item: item[1] is not None,
calc.dict_params.items())))
d['input'] = calc.input_params
d['potcar'] = calc.get_pseudopotentials()
d['atoms'] = atoms_to_dict(calc.get_atoms())
d['data'] = {'doc': 'Data from the output of the calculation'}
atoms = calc.get_atoms()
d['data']['total_energy'] = atoms.get_potential_energy()
d['data']['forces'] = atoms.get_forces().tolist()
# There are times when no stress is calculated
try:
stress = atoms.get_stress()
except NotImplementedError:
stress = None
except AssertionError:
stress = None
if stress is not None:
d['data']['stress'] = atoms.get_stress().tolist()
else:
d['data']['stress'] = None
d['data']['fermi_level'] = calc.get_fermi_level()
d['data']['volume'] = atoms.get_volume()
if calc.spinpol:
d['data']['magmom'] = atoms.get_magnetic_moment()
if (calc.int_params.get('lorbit', 0) >= 10
or calc.list_params.get('rwigs', None)):
try:
d['data']['magmoms'] = atoms.get_magnetic_moments().tolist()
except AttributeError:
d['data']['magmoms'] = None
# store the metadata
if hasattr(calc, 'metadata'):
d['metadata'] = calc.metadata
if kwargs.get('dos', None):
from ase.dft.dos import DOS
dos = DOS(calc, width=kwargs.get('width', 0.2))
e = dos.get_energies()
d['data']['dos'] = {'doc': 'Total density of states'}
d['data']['dos']['e'] = e.tolist()
if calc.spinpol:
d['data']['dos']['dos-up'] = dos.get_dos(spin=0).tolist()
d['data']['dos']['dos-down'] = dos.get_dos(spin=1).tolist()
else:
d['data']['dos']['dos'] = dos.get_dos().tolist()
if kwargs.get('ados', None):
from ase.calculators.vasp import VaspDos
ados = VaspDos(efermi=calc.get_fermi_level())
d['data']['ados'] = {'doc': 'Atom projected DOS'}
nonspin_orbitals_no_phase = ['s', 'p', 'd']
nonspin_orbitals_phase = [
's', 'py', 'pz', 'px', 'dxy', 'dyz', 'dz2', 'dxz', 'dx2'
]
spin_orbitals_no_phase = []
for x in nonspin_orbitals_no_phase:
spin_orbitals_no_phase += ['{0}-up'.format(x)]
spin_orbitals_no_phase += ['{0}-down'.format(x)]
spin_orbitals_phase = []
for x in nonspin_orbitals_phase:
spin_orbitals_phase += ['{0}-up'.format(x)]
spin_orbitals_phase += ['{0}-down'.format(x)]
if calc.spinpol and calc.int_params['lorbit'] != 11:
orbitals = spin_orbitals_no_phase
elif calc.spinpol and calc.int_params['lorbit'] == 11:
orbitals = spin_orbitals_phase
elif calc.int_params['lorbit'] != 11:
orbitals = nonspin_orbitals_no_phase
else:
orbitals = nonspin_orbitals_phase
for i, atom in enumerate(atoms):
d['data']['ados']['energy'] = ados.energy.tolist()
d['data']['ados'][i] = {}
for orbital in orbitals:
d['data']['ados'][i][orbital] = ados.site_dos(
0, orbital).tolist()
# convert all numpy arrays to lists
for key in d:
try:
d[key] = d[key].tolist()
except:
pass
for key in d['input']:
try:
d['input'][key] = d['input'][key].tolist()
except:
pass
return d
save(result_file, 'forces \n {0}'.format(atoms.get_forces()))
calc.set(ismear=-5, lorbit=11, nedos=3001)
p = atoms.get_potential_energy()
save(result_file, '4th calculation \n total energy : {0} eV, {1} eV/atom'.format(p, p/len(atoms)))
tm = atoms.get_magnetic_moment()
m = atoms.get_magnetic_moments()
save(result_file, 'total magnetic moment : {0} mB {1} mB/atom '.format(tm, tm/len(atoms)))
save(result_file, 'magnetic moment: {0}'.format(m))
vdos = VaspDos()
vdos.read_doscar('DOSCAR')
print vdos.efermi
print vdos.site_dos(0,0)
dos = DOS(calc, width=0.05)
d = dos.get_dos()
up = dos.get_dos(0)
down = dos.get_dos(1)
e = dos.get_energies()
plt.plot(e,d, label='total')
plt.plot(e,up, label='spin-up')
plt.plot(e,-1.0*down, label='spin-down')
plt.grid(True)
emax, emin, ngrid, efermi = dos_info('DOSCAR')
vdos = VaspDos()
vdos.read_doscar('DOSCAR')
vdos._set_efermi(efermi)
e = vdos.energy
dos_total = vdos.dos
dos_s = np.zeros(len(e))
dos_p = np.zeros(len(e))
dos_d = np.zeros(len(e))
for i in range(len(atoms)): # atomic type number
dos_s += vdos.site_dos(i,'s')
dos_p += vdos.site_dos(i,'px') + vdos.site_dos(i,'py') + vdos.site_dos(i,'pz')
dos_d += vdos.site_dos(i,'dxy') + vdos.site_dos(i,'dyz') + vdos.site_dos(i,'dz2') + vdos.site_dos(i,'dxz') + vdos.site_dos(i,'dx2')
# dos_s_up = vdos.site_dos(4,'s-up')
# dos_p_up = vdos.site_dos(4,'px-up') + vdos.site_dos(4,'py-up') + vdos.site_dos(4, 'pz-up')
# dos_s_down = vdos.site_dos(0,'s-down')
#dos_p_down = vdos.site_dos(0,'px-down') + vdos.site_dos(0,'py-down') + vdos.site_dos(0,'pz-down')
#dos_d_down = vdos.site_dos(0,'dxy-down') + vdos.site_dos(0,'dyz-down') + vdos.site_dos(0,'dz2-down') + vdos.site_dos(0,'dxz-down') + vdos.site_dos(0,'dx2-down')
plt.plot([-10,10],[0,0],color='black')
plt.plot(e, dos_total, label='total', color='b')
#plt.plot(e, dos_up, label='up', color='r')
#plt.plot(e, -1*dos_down, label='down', color='r')
#
f = open(doscar, "r")
line1 = f.readline()
natom = int(line1.split()[0])
f.close()
dos = VaspDos(doscar=doscar)
ene = dos.energy
tdos = dos.dos
tdos = smear_dos(ene, tdos, sigma=sigma)
if draw_pdos:
pdos = np.zeros(len(tdos))
for i in range(0, natom):
pdos = pdos + dos.site_dos(i, orbital)
pdos = smear_dos(ene, pdos, sigma=sigma)
sb.set(context='notebook',
style='darkgrid',
palette='deep',
font='sans-serif',
font_scale=1,
color_codes=False,
rc=None)
#plt.plot(ene, tdos,"r-",linewidth=2)
plt.plot(ene, tdos)
filename = "DOS_" + system + ".png"
plt.ylabel("Density of state (-)")
plt.xlabel("Energy (eV)")
lattice = obj.lattice
data = obj.data
#
# limit analysis only for occupied part
#
margin = 0.0
ene = list(filter(lambda x: x <= efermi + margin, ene))
for orbital in orbitals:
#
# get pdos for total system
#
pdos_tot = np.zeros(len(ene))
tmpdos = np.zeros(len(ene))
for i in range(0, natom):
tmpdos = tmpdos + dos.site_dos(i, orbital)[:len(ene)]
tmpdos = tmpdos[:len(ene)]
tmpdos = tmpdos / np.max(tmpdos) if normalize_height else tmpdos
pdos_tot = smear_dos(ene, tmpdos, sigma=sigma)
integ = get_distribution_moment(ene, tmpdos, order=0)
center = get_distribution_moment(ene, tmpdos, order=1)
second = get_distribution_moment(ene, tmpdos, order=2)
third = get_distribution_moment(ene, tmpdos, order=3)
fourth = get_distribution_moment(ene, tmpdos, order=4)
#
# get pdos for surface layer
#
pdos_surf = np.zeros(len(ene))
tmpdos = np.zeros(len(ene))
for i in range(48, 64):
tmpdos = tmpdos + dos.site_dos(i, orbital)[:len(ene)]
elif o == 'd': orbitals = d_up + d_down
elif o == 'f': orbitals = f_up + f_down
elif o == 'all': orbitals = all_up + all_down
else: orbitals = [o]
elif options.spin == "+":
if o == 's': orbitals = s_up
elif o == 'p': orbitals = p_up
elif o == 'd': orbitals = d_up
elif o == 'f': orbitals = f_up
elif o == 'all': orbitals = all_up
else: orbitals = [o]
elif options.spin == "-":
if o == 's': orbitals = s_down
elif o == 'p': orbitals = p_down
elif o == 'd': orbitals = d_down
elif o == 'f': orbitals = f_down
elif o == 'all': orbitals = all_down
else: orbitals = [o]
# print range(a[0], a[1]+1)
for orbit in orbitals:
for i in range(a[0] - 1, a[1]):
dos = dos + doscar.site_dos(i, orbit)
for i in range(len(energy)):
l_en = energy[i] - options.ferm
l_dos = dos[i]
if (options.per_atom == "True"):
l_dos = l_dos / float(a[1] - a[0] + 1)
# print l_en,l_dos
print l_en, sign * dos[i]