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.
'''
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
