def dos(filename, plot=False, output='dos.csv', width=0.1):
"""Calculate density of states.
filename: str
Name of restart-file.
plot: bool
Show a plot.
output: str
Name of CSV output file.
width: float
Width of Gaussians.
"""
calc = GPAW(filename, txt=None)
dos = DOS(calc, width)
D = [dos.get_dos(spin) for spin in range(calc.get_number_of_spins())]
if output:
fd = sys.stdout if output == '-' else open(output, 'w')
for x in zip(dos.energies, *D):
print(*x, sep=', ', file=fd)
if output != '-':
fd.close()
if plot:
import matplotlib.pyplot as plt
for y in D:
plt.plot(dos.energies, y)
plt.show()
def dos(filename, plot=False, output='dos.csv', width=0.1):
"""Calculate density of states.
filename: str
Name of restart-file.
plot: bool
Show a plot.
output: str
Name of CSV output file.
width: float
Width of Gaussians.
"""
from gpaw import GPAW
from ase.dft.dos import DOS
calc = GPAW(filename, txt=None)
dos = DOS(calc, width)
D = [dos.get_dos(spin) for spin in range(calc.get_number_of_spins())]
if output:
fd = sys.stdout if output == '-' else open(output, 'w')
for x in zip(dos.energies, *D):
print(*x, sep=', ', file=fd)
if output != '-':
fd.close()
if plot:
import matplotlib.pyplot as plt
for y in D:
plt.plot(dos.energies, y)
plt.show()
def get_dos(self, spin=None, **kwargs):
"""
The total DOS.
Uses the ASE DOS module, and returns a tuple with
(energies, dos).
"""
from ase.dft.dos import DOS
dos = DOS(self, **kwargs)
e = dos.get_energies()
d = dos.get_dos(spin=spin)
return e, d
def create_ase_object(objtype, dct):
# We just try each object type one after another and instantiate
# them manually, depending on which kind it is.
# We can formalize this later if it ever becomes necessary.
if objtype == 'cell':
from ase.cell import Cell
dct.pop('pbc', None) # compatibility; we once had pbc
obj = Cell(**dct)
elif objtype == 'bandstructure':
from ase.spectrum.band_structure import BandStructure
obj = BandStructure(**dct)
elif objtype == 'bandpath':
from ase.dft.kpoints import BandPath
obj = BandPath(path=dct.pop('labelseq'), **dct)
elif objtype == 'atoms':
from ase import Atoms
obj = Atoms.fromdict(dct)
elif objtype == 'densityofstates':
from ase.dft.dos import DOS
obj = DOS(**dct)
elif objtype == 'griddoscollection':
from ase.spectrum.doscollection import GridDOSCollection
obj = GridDOSCollection.fromdict(dct)
else:
raise ValueError('Do not know how to decode object type {} '
'into an actual object'.format(objtype))
assert obj.ase_objtype == objtype
return obj
def get_dos(self, width=0.15, method='gaussian', npts=501):
"""
density of states.
:param width: smearing width
:param method: 'gaussian'| 'tetra'
:param npts: number of DOS energies.
:returns:
energies, dos. two ndarray.
TODO: implement spin resolved DOS.
"""
if method == 'tetra':
dos = tetrahedronDosClass(self, width, npts=npts)
else:
dos = DOS(self, width, window=None, npts=npts)
return dos.get_energies(), dos.get_dos()
def get_dos(self, width=None, smearing='gaussian', npts=501):
"""
density of states.
:param width: smearing width
:param method: 'gaussian'| 'tetra'
:param npts: number of DOS energies.
:returns:
energies, dos. two ndarray.
TODO: implement spin resolved DOS.
"""
if width is None:
width = self._width
if smearing == 'tetra':
raise NotImplementedError('tetrahedron DOS not implemented')
#dos = tetrahedronDosClass(self, width, npts=npts)
else:
dos = DOS(self, width, window=None, npts=npts)
return dos.get_energies(), dos.get_dos()
def test_dos():
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.calculators.singlepoint import SinglePointKPoint
from ase.dft.dos import DOS
atoms = Atoms('H')
eFermi = [0, 1]
kpts = [SinglePointKPoint(1, 0, 0), SinglePointKPoint(1, 1, 0)]
kpts[0].eps_n = [-2, -1, 1]
kpts[0].f_n = [1, 0, 0]
kpts[1].eps_n = [-2.5, -1.5, 0.5]
kpts[1].f_n = [1, 0, 0]
calc = SinglePointDFTCalculator(atoms, efermi=eFermi)
calc.kpts = kpts
DOS(calc)
def get_dos(self,kpoints=None,width=0.1,window=None,npts=201,spin=None):
"""
calculate density of states.
:param kpoints: set k-points for DOS calculation.
:param width: smearing width
:param window: energy windown. e.g. [-5,5]
:param npts: number of points.
:param spin: No use here. Just to keep with the ase API.
"""
if kpoints is not None:
self.params['calculation']='nscf'
self.kpts=['automatic',kpoints]
self.params['occupations']='tetrahedra'
self.initialize(self.atoms)
self.calculate()
self.read_output()
mydos=DOS(self,width=width,window=window,npts=201)
self.dos_energies=mydos.get_energies()
self.dos=mydos.get_dos()
if self.spin_polarized:
self.dos_up=mydos.get_dos(spin=0)
self.dos_down=mydos.get_dos(spin=1)
from jasp import *
from ase.dft.dos import DOS
import matplotlib.pyplot as plt
with jasp('molecules/simple-co') as calc: # we already ran this!
dos = DOS(calc)
plt.plot(dos.get_energies(), dos.get_dos())
plt.xlabel('Energy - $E_f$ (eV)')
plt.ylabel('DOS')
# make sure you save the figure outside the with statement, or provide
# the correct relative or absolute path to where you want it.
plt.savefig('images/co-dos.png')
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.calculators.singlepoint import SinglePointKPoint
from ase.dft.dos import DOS
atoms = Atoms('H')
eFermi = [0, 1]
kpts = [SinglePointKPoint(1, 0, 0), SinglePointKPoint(1, 1, 0)]
kpts[0].eps_n = [-2, -1, 1]
kpts[0].f_n = [1, 0, 0]
kpts[1].eps_n = [-2.5, -1.5, 0.5]
kpts[1].f_n = [1, 0, 0]
calc = SinglePointDFTCalculator(atoms, efermi=eFermi)
calc.kpts = kpts
dos = DOS(calc)
class BandStructure:
'''outline of class to facilitate band structure calculations
'''
def __init__(self, atoms, BZpath=[], npoints=10, outnc='harris.nc'):
"""Headline here ... XXX.
atoms is an ase.Atoms object with calculator
attached. Presumably the self-consistent charge density has
already been calculated, otherwise, it will be.
BZpath is a list of tuples describing the path through the
Brillouin zone. The tuples have the form (label, kpt), e.g. ::
[('$\Gamma$',[0.0, 0.0, 0.0]),
('X',[0.0, 0.5, 0.5]),
('L',[0.5, 0.0, 0.0]),
('$\Gamma$',[0.0, 0.0, 0.0])]
the label is used in the figure and can include latex markup.
npoints is the number of points on each segment. It can either
be a constant, which is used for every segment, or a list of
integers that is an integer for each segment.
"""
self.atoms = atoms
self.calc = atoms.get_calculator()
#first, we make sure the charge density is up to date.
self.calc.get_charge_density()
self.ef = self.calc.get_ef() #self-consistent fermi level
self.labels = [x[0] for x in BZpath]
self.kpt_path = [np.array(x[1], dtype=np.float) for x in BZpath]
self.npoints = npoints
#first, setup the kpt path
kpts = []
#start at second kpt and go to second to last segment
nsegments = len(self.kpt_path) - 1
for i in range(nsegments - 1):
#get number of points on path. this counts the first point
try:
i_npt = npoints[i]
except TypeError:
i_npt = npoints
#this is the vector connecting the two endpoint kpts of a segment
kdiff = self.kpt_path[i + 1] - self.kpt_path[i]
#make a vector of evenly spaced intervals, one longer than needed
#because we chop off the last entry.
for j in np.linspace(0, 1, i_npt + 1)[0:-1]:
k = self.kpt_path[i] + j * kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3)) / 1.e4
k += krand
kpts.append(k)
#now fill in the last segment, and end on the last point
try:
i_npt = npoints[-1]
except TypeError:
i_npt = npoints
kdiff = self.kpt_path[-1] - self.kpt_path[-2]
for j in np.linspace(0, 1, i_npt + 1)[1:]:
k = self.kpt_path[-2] + j * kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3)) / 1.e4
k += krand
kpts.append(k)
#these are now the points needed for the Harris calculation.
self.kpts = kpts
self.dos = DOS(self.calc)
self.dos_energies = self.dos.get_energies()
self.dos_dos = self.dos.get_dos()
#try to avoid rerunning the calculation if it is already done!
if os.path.exists(outnc):
self.calc = Jacapo(outnc)
else:
print('calculation of harris required')
self.calc.set_nc(outnc)
#self.calc.debug=10
#save some time by not calculating stress
self.calc.set_stress(False)
#this seems to be necessary sometimes
self.calc.delete_ncattdimvar(outnc, ncdims=['number_plane_waves'])
#this has to come after removing number_of_planewaves
self.calc.set_kpts(self.kpts)
#freeze charge density
self.calc.set_charge_mixing(updatecharge='No')
#and, run calculation
self.calc.calculate()
def plot(self):
'''
Make an interactive band-structure plot.
clicking on a band will make it thicker and print which band was selected.
'''
# kpoints = self.calc.get_ibz_kpoints()
eigenvalues = self.calc.get_all_eigenvalues() - self.ef
#eigenvalues = np.array([self.calc.get_eigenvalues(kpt=i)-self.ef
# for i in range(len(kpoints))])
self.handles = [] #used to get band indexes from plot
fig = plt.figure()
#plot DOS in figure
ax = fig.add_subplot(122)
ax.plot(self.dos_dos, self.dos_energies)
plt.title('self-consistent Total DOS')
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylim([-20, 20])
ax = fig.add_subplot(121)
ax.set_title('Band structure')
def onpick(event):
'make picked line bolder, set oldline back to regular thickness'
self.lastartist.set_linewidth(1)
self.lastartist = thisline = event.artist
thisline.set_linewidth(5)
plt.draw() #needed to update linewidth
print('Band %i selected' % self.handles.index(thisline))
#you could insert code here to plot wavefunction, etc...
fig.canvas.mpl_connect('pick_event', onpick)
#we use indices for x. the tick labels are not shown and the distance
#appears unimportant
xdata = list(range(len(eigenvalues)))
nkpts, nbands = eigenvalues.shape
for i in range(nbands):
#eigenvalues has shape(nkpts,nbands)
#note the comma after line_handle
line_handle, = ax.plot(xdata,
eigenvalues[:, i],
'.-',
ms=1,
picker=2)
self.handles.append(line_handle)
self.lastartist = self.handles[-1]
#plot Fermi level
ax.plot([0, len(self.kpts)], [0, 0], 'k--', label='$E_f$')
plt.xlabel('|k|')
plt.ylabel('$E-E_f$ (eV)')
#set xtick locations and labels
xtick_locs = np.zeros(len(self.kpt_path))
try:
#this means the npoints is a list
# i_npt = self.npoints[0]
for j, npt in enumerate(1, self.npoints):
xtick_locs[j] = xtick_locs[j - 1] + npt
except TypeError:
#npoints is a single number
for j in range(1, len(self.labels)):
xtick_locs[j] = xtick_locs[j - 1] + self.npoints
#the last location is off by one, so we fix it.
xtick_locs[-1] -= 1
ax.set_xlim([xtick_locs[0], xtick_locs[-1]])
ax.set_xticks(xtick_locs)
ax.set_xticklabels(self.labels)
#this seems reasonable to avoid very deep energy states and high energy states
ax.set_ylim([-20, 20])
plt.show()
return fig
def __init__(self, atoms, BZpath=[], npoints=10, outnc='harris.nc'):
"""Headline here ... XXX.
atoms is an ase.Atoms object with calculator
attached. Presumably the self-consistent charge density has
already been calculated, otherwise, it will be.
BZpath is a list of tuples describing the path through the
Brillouin zone. The tuples have the form (label, kpt), e.g. ::
[('$\Gamma$',[0.0, 0.0, 0.0]),
('X',[0.0, 0.5, 0.5]),
('L',[0.5, 0.0, 0.0]),
('$\Gamma$',[0.0, 0.0, 0.0])]
the label is used in the figure and can include latex markup.
npoints is the number of points on each segment. It can either
be a constant, which is used for every segment, or a list of
integers that is an integer for each segment.
"""
self.atoms = atoms
self.calc = atoms.get_calculator()
#first, we make sure the charge density is up to date.
self.calc.get_charge_density()
self.ef = self.calc.get_ef() #self-consistent fermi level
self.labels = [x[0] for x in BZpath]
self.kpt_path = [np.array(x[1], dtype=np.float) for x in BZpath]
self.npoints = npoints
#first, setup the kpt path
kpts = []
#start at second kpt and go to second to last segment
nsegments = len(self.kpt_path) - 1
for i in range(nsegments - 1):
#get number of points on path. this counts the first point
try:
i_npt = npoints[i]
except TypeError:
i_npt = npoints
#this is the vector connecting the two endpoint kpts of a segment
kdiff = self.kpt_path[i + 1] - self.kpt_path[i]
#make a vector of evenly spaced intervals, one longer than needed
#because we chop off the last entry.
for j in np.linspace(0, 1, i_npt + 1)[0:-1]:
k = self.kpt_path[i] + j * kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3)) / 1.e4
k += krand
kpts.append(k)
#now fill in the last segment, and end on the last point
try:
i_npt = npoints[-1]
except TypeError:
i_npt = npoints
kdiff = self.kpt_path[-1] - self.kpt_path[-2]
for j in np.linspace(0, 1, i_npt + 1)[1:]:
k = self.kpt_path[-2] + j * kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3)) / 1.e4
k += krand
kpts.append(k)
#these are now the points needed for the Harris calculation.
self.kpts = kpts
self.dos = DOS(self.calc)
self.dos_energies = self.dos.get_energies()
self.dos_dos = self.dos.get_dos()
#try to avoid rerunning the calculation if it is already done!
if os.path.exists(outnc):
self.calc = Jacapo(outnc)
else:
print('calculation of harris required')
self.calc.set_nc(outnc)
#self.calc.debug=10
#save some time by not calculating stress
self.calc.set_stress(False)
#this seems to be necessary sometimes
self.calc.delete_ncattdimvar(outnc, ncdims=['number_plane_waves'])
#this has to come after removing number_of_planewaves
self.calc.set_kpts(self.kpts)
#freeze charge density
self.calc.set_charge_mixing(updatecharge='No')
#and, run calculation
self.calc.calculate()
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
def dos(filename, plot=False, output='dos.csv', width=0.1, integrated=False,
projection=None, emin=None, emax=None, npoints=400, show_total=None):
"""Calculate density of states.
filename: str
Name of restart-file.
plot: bool
Show a plot.
output: str
Name of CSV output file.
width: float
Width of Gaussians.
integrated: bool
Calculate integrated DOS.
"""
calc = GPAW(filename, txt=None)
dos = DOS(calc, width, (emin, emax), npoints)
nspins = calc.get_number_of_spins()
spinlabels = [''] if nspins == 1 else [' up', ' dn']
if projection is None or show_total:
D = [dos.get_dos(spin) for spin in range(nspins)]
labels = ['DOS' + sl for sl in spinlabels]
else:
D = []
labels = []
if projection is not None:
for p in projection.split(','):
s, ll = p.split('-')
if s.isdigit():
A = [int(s)]
s = '#' + s
else:
A = [a for a, symbol in
enumerate(calc.atoms.get_chemical_symbols())
if symbol == s]
if not A:
raise ValueError('No such atom: ' + s)
for spin in range(nspins):
for l in ll:
d = 0.0
for a in A:
d += ldos(calc, a, spin, l, width, dos.energies)
labels.append(s + '-' + l + spinlabels[spin])
D.append(d)
if integrated:
de = dos.energies[1] - dos.energies[0]
dos.energies += de / 2
D = [np.cumsum(d) * de for d in D]
ylabel = 'iDOS [electrons]'
else:
ylabel = 'DOS [electrons/eV]'
if output:
fd = sys.stdout if output == '-' else open(output, 'w')
for x in zip(dos.energies, *D):
print(*x, sep=', ', file=fd)
if output != '-':
fd.close()
if plot:
import matplotlib.pyplot as plt
for y, label in zip(D, labels):
plt.plot(dos.energies, y, label=label)
plt.legend()
plt.ylabel(ylabel)
plt.xlabel(r'$\epsilon-\epsilon_F$ [eV]')
plt.show()
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
# Get band structure and dos
Ebs = atoms.calc.band_structure() # Get the band structure
# if world.rank == 0:
print('Electronic band structure calculated')
kpts = {'size': (40,40,40)}
calc.set(
kpts = kpts,
fixdensity=True,
symmetry='off',
)
# Fix the potential
calc.get_potential_energy()
# e, dos = calc.get_dos(spin=0, npts=1001, width=0.5) # Get energy and density of states
dos = DOS(calc, npts=2000, width=0.1)
d = dos.get_dos()
e = dos.get_energies()
f = calc.get_fermi_level()
print('Electronic DOS computed')
e_f = calc.get_fermi_level()
Edos = {
'e': e,
'dos': d,
'fermi': e_f
}
# Save results
pickle.dump( Ebs, open( "Ebs.p", "wb" ) ) # Save the electronic band structure
pickle.dump( Edos, open( "Edos.p", "wb" ) ) # Save the electronic DOS
# if world.rank == 0:
def add_to_plot(self, readoutfilesobj, label=None):
"""
|Here you add individual plots that need to be plot and then just plot them with the plot() method
|Use this method which is a part of the BandPlotterASE class you will have to give the bands to plot using a readoutfilesobj type of object
"""
try:
Ef = readoutfilesobj.atoms_objects[0].calc.get_fermi_level()
except:
print(f"add_to_plot: Could not read fermi level on scf file")
try:
kpts = readoutfilesobj.atoms_bands_objects[
0].calc.get_ibz_k_points()
except:
print(f"add_to_plot: Could not read k points on bands file")
if self.include_dos or self.plot_only_dos:
if self.plot_from_QE_dos_file:
E = []
dos = []
with open(readoutfilesobj.dos_file_name, "r") as dos_file:
for line in dos_file:
# print(line)
if "#" not in line:
data = line.strip().split()
E.append(float(data[0]) - Ef)
dos.append(float(data[1]))
# self.y_to_plot.append(dos)
# self.x_to_plot.append(E)
self.dos.append(dos)
self.E_dos.append(E)
if self.plot_only_dos: # Other wise we wil lappend to labels twice sicnce we will do it again at theloading of bands
self.labels.append(label)
else:
# we are here getting the required information for DOS
# self.get_dos(readoutfilesobj)
calc = readoutfilesobj.atoms_nscf_objects[0].calc
Ef_nscf = readoutfilesobj.atoms_nscf_objects[
0].calc.get_fermi_level()
dos = DOS(calc, width=0.2)
self.dos.append(dos.get_dos())
E_nscf = dos.get_energies()
Ef_diff = Ef - Ef_nscf
if abs(Ef_diff) >= 0.001:
print(
f"Warning!!! In {readoutfilesobj.identifier[0]}:\t|E_f_scf-E_f_nscf| = {abs(Ef_diff):.3} eV (>= 0.001 eV); E_f_scf = {Ef} eV, E_f_nscf = {Ef_nscf} eV"
)
if self.pin_fermi != "scf": self.E_dos.append(E_nscf)
else: self.E_dos.append([E - Ef_diff for E in E_nscf])
# Test space for k path and k high symmetry points
# print(kpts)
# print(self.plot_only_dos)
if self.plot_only_dos == False:
# This is for teh band structure
path = readoutfilesobj.atoms_bands_objects[0].cell.bandpath(
npoints=0)
kinks = find_bandpath_kinks(
readoutfilesobj.atoms_bands_objects[0].cell, kpts,
eps=1e-5) # These are the high symmetry points in use
pathspec = resolve_custom_points(
kpts[kinks], path.special_points, eps=1e-5
) # This gives the postions for the relevant high symmetry points
# path.kpts = kpts
# path.path = pathspec
klengths = []
for x in range(0, len(kpts)):
if x == 0:
kdist = np.sqrt((0.0 - kpts[x][0])**2 +
(0.0 - kpts[x][1])**2 +
(0.0 - kpts[x][2])**2)
klengths.append(kdist)
else:
kdist = np.sqrt((kpts[x - 1][0] - kpts[x][0])**2 +
(kpts[x - 1][1] - kpts[x][1])**2 +
(kpts[x - 1][2] - kpts[x][2])**2)
klengths.append(kdist + klengths[x - 1])
self.k_locations = []
for x in range(len(kinks)):
self.k_locations.append(klengths[kinks[x]])
self.k_symbols = []
for x in pathspec:
if x == "G":
self.k_symbols.append("$\Gamma$")
else:
self.k_symbols.append(x)
energies = []
for s in range(readoutfilesobj.atoms_bands_objects[0].calc.
get_number_of_spins()):
energies.append([
readoutfilesobj.atoms_bands_objects[0].calc.
get_eigenvalues(kpt=k, spin=s) for k in range(len(kpts))
])
# print(f"lenght of kpoints: {range(len(kpts))}")
Energy_to_plot = []
if self.Ef_shift == True:
for band in energies[0]:
if self.pin_fermi != "nscf":
Energy_to_plot.append([E - Ef for E in band])
else:
Energy_to_plot.append(
[E - Ef_nscf for E in band]
) # here the assumption is that if this option is ever reached then the idea is that an nscf calculation has already being done and dos is being plotted.
tempMain = []
temp = []
for x in range(len(Energy_to_plot[0])):
for kpoint in Energy_to_plot:
temp.append(kpoint[x])
tempMain.append(temp)
temp = []
self.y_to_plot.append(tempMain)
self.x_to_plot.append(klengths)
self.labels.append(label)
import matplotlib.pyplot as plt
from gpaw import GPAW
from ase.dft.dos import DOS
calc = GPAW('groundstate.gpw')
dos = DOS(calc, npts=800, width=0.1)
energies = dos.get_energies()
weights = dos.get_dos()
ax = plt.gca()
ax.plot(energies, weights)
ax.set_xlabel(r'$E - E_{\mathrm{Fermi}}$ [eV]')
ax.set_ylabel('DOS [1/eV]')
plt.savefig('dos.png')
plt.show()
start = time.time()
# if world.rank == 0:
print(f'Calculating EOS for Al{N}')
# Define electron calculator (GPAW)
calc = GPAW(
mode=PW(300), # Lower for computational efficiency
txt=f'./gpaw-out/EOS_{N}_1core.txt'
) # Use the same calculator as in task6
atoms.set_calculator(calc)
pot_e = atoms.get_potential_energy() # Self-constistently optimize the electron density
# if world.rank == 0:
print(f'Cluster Al{N} finished potential energy per atom: {pot_e / N:.2f} eV')
# Get the electronic DOS
dos = DOS(calc, npts=800, width=0.2)
e = dos.get_energies()
d = dos.get_dos()
e_f = calc.get_fermi_level()
e -= e_f # Subtract the Fermi level from the energy
##### Get the DOS using the same method as in task6
# print('Electronic band structure calculated')
# kpts = {'size': (40,40,40)}
# calc.set(
# kpts = kpts,
# fixdensity=True,
# symmetry='off',
# )
# # Fix the potential
from jasp import *
from ase.dft.dos import DOS
import matplotlib.pyplot as plt
# get the geometry from another calculation
with jasp('molecules/simple-co') as calc:
atoms = calc.get_atoms()
with jasp(
'molecules/co-ados',
encut=300,
xc='PBE',
rwigs=[1.0, 1.0], # these are the cutoff radii for projected states
atoms=atoms) as calc:
calc.calculate()
# now get results
dos = DOS(calc)
plt.plot(dos.get_energies(), dos.get_dos() + 10)
ados = VaspDos(efermi=calc.get_fermi_level())
energies = ados.energy
plt.plot(energies, ados.dos + 8, label='ADOS') # these are the total DOS
c_s = ados.site_dos(0, 's')
c_p = ados.site_dos(0, 'p')
o_s = ados.site_dos(1, 's')
o_p = ados.site_dos(1, 'p')
c_d = ados.site_dos(0, 'd')
o_d = ados.site_dos(1, 'd')
plt.plot(energies, c_s + 6, energies, o_s + 5)
plt.plot(energies, c_p + 4, energies, o_p + 3)
plt.plot(energies, c_d, energies, o_d + 2)
plt.xlabel('Energy - $E_f$ (eV)')
plt.ylabel('DOS')
plt.legend(
def __init__(self,
atoms,
BZpath=[],
npoints=10,
outnc='harris.nc'):
"""Headline here ... XXX.
atoms is an ase.Atoms object with calculator
attached. Presumably the self-consistent charge density has
already been calculated, otherwise, it will be.
BZpath is a list of tuples describing the path through the
Brillouin zone. The tuples have the form (label, kpt), e.g. ::
[('$\Gamma$',[0.0, 0.0, 0.0]),
('X',[0.0, 0.5, 0.5]),
('L',[0.5, 0.0, 0.0]),
('$\Gamma$',[0.0, 0.0, 0.0])]
the label is used in the figure and can include latex markup.
npoints is the number of points on each segment. It can either
be a constant, which is used for every segment, or a list of
integers that is an integer for each segment.
"""
self.atoms = atoms
self.calc = atoms.get_calculator()
#first, we make sure the charge density is up to date.
self.calc.get_charge_density()
self.ef = self.calc.get_ef() #self-consistent fermi level
self.labels = [x[0] for x in BZpath]
self.kpt_path = [np.array(x[1],dtype=np.float) for x in BZpath]
self.npoints = npoints
#first, setup the kpt path
kpts = []
#start at second kpt and go to second to last segment
nsegments = len(self.kpt_path) - 1
for i in range(nsegments-1):
#get number of points on path. this counts the first point
try:
i_npt = npoints[i]
except TypeError:
i_npt = npoints
#this is the vector connecting the two endpoint kpts of a segment
kdiff = self.kpt_path[i+1] - self.kpt_path[i]
#make a vector of evenly spaced intervals, one longer than needed
#because we chop off the last entry.
for j in np.linspace(0,1,i_npt+1)[0:-1]:
k = self.kpt_path[i] + j*kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3))/1.e4
k += krand
kpts.append(k)
#now fill in the last segment, and end on the last point
try:
i_npt = npoints[-1]
except TypeError:
i_npt = npoints
kdiff = self.kpt_path[-1] - self.kpt_path[-2]
for j in np.linspace(0,1,i_npt+1)[1:]:
k = self.kpt_path[-2] + j*kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3))/1.e4
k += krand
kpts.append(k)
#these are now the points needed for the Harris calculation.
self.kpts = kpts
self.dos = DOS(self.calc)
self.dos_energies = self.dos.get_energies()
self.dos_dos = self.dos.get_dos()
#try to avoid rerunning the calculation if it is already done!
if os.path.exists(outnc):
self.calc = Jacapo(outnc)
else:
print 'calculation of harris required'
self.calc.set_nc(outnc)
#self.calc.debug=10
#save some time by not calculating stress
self.calc.set_stress(False)
#this seems to be necessary sometimes
self.calc.delete_ncattdimvar(outnc,
ncdims=['number_plane_waves'])
#this has to come after removing number_of_planewaves
self.calc.set_kpts(self.kpts)
#freeze charge density
self.calc.set_charge_mixing(updatecharge='No')
#and, run calculation
self.calc.calculate()
class BandStructure:
'''outline of class to facilitate band structure calculations
'''
def __init__(self,
atoms,
BZpath=[],
npoints=10,
outnc='harris.nc'):
"""Headline here ... XXX.
atoms is an ase.Atoms object with calculator
attached. Presumably the self-consistent charge density has
already been calculated, otherwise, it will be.
BZpath is a list of tuples describing the path through the
Brillouin zone. The tuples have the form (label, kpt), e.g. ::
[('$\Gamma$',[0.0, 0.0, 0.0]),
('X',[0.0, 0.5, 0.5]),
('L',[0.5, 0.0, 0.0]),
('$\Gamma$',[0.0, 0.0, 0.0])]
the label is used in the figure and can include latex markup.
npoints is the number of points on each segment. It can either
be a constant, which is used for every segment, or a list of
integers that is an integer for each segment.
"""
self.atoms = atoms
self.calc = atoms.get_calculator()
#first, we make sure the charge density is up to date.
self.calc.get_charge_density()
self.ef = self.calc.get_ef() #self-consistent fermi level
self.labels = [x[0] for x in BZpath]
self.kpt_path = [np.array(x[1],dtype=np.float) for x in BZpath]
self.npoints = npoints
#first, setup the kpt path
kpts = []
#start at second kpt and go to second to last segment
nsegments = len(self.kpt_path) - 1
for i in range(nsegments-1):
#get number of points on path. this counts the first point
try:
i_npt = npoints[i]
except TypeError:
i_npt = npoints
#this is the vector connecting the two endpoint kpts of a segment
kdiff = self.kpt_path[i+1] - self.kpt_path[i]
#make a vector of evenly spaced intervals, one longer than needed
#because we chop off the last entry.
for j in np.linspace(0,1,i_npt+1)[0:-1]:
k = self.kpt_path[i] + j*kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3))/1.e4
k += krand
kpts.append(k)
#now fill in the last segment, and end on the last point
try:
i_npt = npoints[-1]
except TypeError:
i_npt = npoints
kdiff = self.kpt_path[-1] - self.kpt_path[-2]
for j in np.linspace(0,1,i_npt+1)[1:]:
k = self.kpt_path[-2] + j*kdiff
#shift by small random amount to break symmetry and
#prevent time-inversion reduction
krand = (1. + np.random.random(3))/1.e4
k += krand
kpts.append(k)
#these are now the points needed for the Harris calculation.
self.kpts = kpts
self.dos = DOS(self.calc)
self.dos_energies = self.dos.get_energies()
self.dos_dos = self.dos.get_dos()
#try to avoid rerunning the calculation if it is already done!
if os.path.exists(outnc):
self.calc = Jacapo(outnc)
else:
print 'calculation of harris required'
self.calc.set_nc(outnc)
#self.calc.debug=10
#save some time by not calculating stress
self.calc.set_stress(False)
#this seems to be necessary sometimes
self.calc.delete_ncattdimvar(outnc,
ncdims=['number_plane_waves'])
#this has to come after removing number_of_planewaves
self.calc.set_kpts(self.kpts)
#freeze charge density
self.calc.set_charge_mixing(updatecharge='No')
#and, run calculation
self.calc.calculate()
def plot(self):
'''
Make an interactive band-structure plot.
clicking on a band will make it thicker and print which band was selected.
'''
kpoints = self.calc.get_ibz_kpoints()
eigenvalues = self.calc.get_all_eigenvalues() - self.ef
#eigenvalues = np.array([self.calc.get_eigenvalues(kpt=i)-self.ef
# for i in range(len(kpoints))])
self.handles = [] #used to get band indexes from plot
fig = plt.figure()
#plot DOS in figure
ax = fig.add_subplot(122)
ax.plot(self.dos_dos,self.dos_energies)
plt.title('self-consistent Total DOS')
ax.set_xticks([])
ax.set_yticks([])
ax.set_ylim([-20,20])
ax = fig.add_subplot(121)
ax.set_title('Band structure')
def onpick(event):
'make picked line bolder, set oldline back to regular thickness'
self.lastartist.set_linewidth(1)
self.lastartist = thisline = event.artist
thisline.set_linewidth(5)
plt.draw() #needed to update linewidth
print 'Band %i selected' % self.handles.index(thisline)
#you could insert code here to plot wavefunction, etc...
fig.canvas.mpl_connect('pick_event',onpick)
#we use indices for x. the tick labels are not shown and the distance
#appears unimportant
xdata = range(len(eigenvalues))
nkpts, nbands = eigenvalues.shape
for i in range(nbands):
#eigenvalues has shape(nkpts,nbands)
#note the comma after line_handle
line_handle, = ax.plot(xdata,eigenvalues[:,i],'.-',ms=1,picker=2)
self.handles.append(line_handle)
self.lastartist = self.handles[-1]
#plot Fermi level
ax.plot([0,len(self.kpts)],[0,0],'k--',label='$E_f$')
plt.xlabel('|k|')
plt.ylabel('$E-E_f$ (eV)')
#set xtick locations and labels
xtick_locs = np.zeros(len(self.kpt_path))
try:
#this means the npoints is a list
i_npt = self.npoints[0]
for j,npt in enumerate(1,self.npoints):
xtick_locs[j] = xtick_locs[j-1] + npt
except TypeError:
#npoints is a single number
for j in range(1,len(self.labels)):
xtick_locs[j] = xtick_locs[j-1] + self.npoints
#the last location is off by one, so we fix it.
xtick_locs[-1] -= 1
ax.set_xlim([xtick_locs[0],xtick_locs[-1]])
ax.set_xticks(xtick_locs)
ax.set_xticklabels(self.labels)
#this seems reasonable to avoid very deep energy states and high energy states
ax.set_ylim([-20,20])
plt.show()
return fig
testRun = False
file_name_py = basename(__file__)
file_name = file_name_py.replace('.py','')
file_traj = file_name + '.traj'
start_file = '../In2O3_110_clean.traj'
try:
sys = Trajectory(file_traj, 'r')[-1]
except (IOError, RuntimeError):
print(("Importing trajectory file from: %s" % start_file))
sys = read(start_file)
else:
print(("Importing trajectory file from: %s" % file_traj))
calc = set_calc_In2O3(sys)
print("Constraints:")
print("\tc: Fix bottom two layers.")
c = FixAtoms(mask=[atom.z < 8 for atom in sys])
sys.set_constraint(c)
if testRun == True:
run_testRun(sys)
else:
dos = DOS(calc = calc)
ds = dos.get_dos()
es = dos.get_energies()
print("Energy\tDOS")
for (e, d) in zip(es, ds):
print(("%f\t%f" % (e, d)))
print(("Completed %s" % file_name_py))
'''Write DOS to JSON file, starting from GPAW calculator file.
'''
import sys
import json
from gpaw import GPAW
from ase.dft.dos import DOS
if len(sys.argv) != 2:
raise RuntimeError('I want one and only one argument, the filename!')
filename = sys.argv[1]
calc = GPAW(filename, txt=None)
dos = DOS(calc, width=0.1)
dos_dict = {}
dos_dict['dos'] = list(dos.get_dos())
dos_dict['energies'] = list(dos.get_energies())
out_name = filename + '_dos.json'
with open(out_name, 'w') as outfile:
json.dump(dos_dict, outfile)
print('DOS written to', out_name)