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dft_tools
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Fix error in transport code, some modifications

This commit is contained in:
Manuel Zingl 2015-02-18 00:27:00 +01:00
parent 674059506f
commit 373764f680
5 changed files with 34 additions and 29 deletions
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8
doc/Transport.rst
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@ -85,10 +85,12 @@ First we have to read the Wien2k files and store the relevant information in the
SK = SumkDFTTools(hdf_file='case.h5', use_dft_blocks=True)
Additionally we need to read and set the self energy::
Additionally we need to read and set the self energy, the chemical potential and the double counting::
ar = HDFArchive('case_Sigma.h5', 'a')
SK.put_Sigma(Sigma_imp = [ar['dmft_transp_output']['Sigma_w']])
SK.chemical_potential = ar['dmft_transp_output']['chemical_potential']
SK.dc_imp = ar['dmft_transp_output']['dc_imp']
del ar
As next step we can calculate the transport distribution :math:`\Gamma_{\alpha\beta}(\omega)`::
@ -100,8 +102,8 @@ The parameters are:
* `directions`: :math:`\alpha` and :math:`\beta` (e.g. xx, yy, xz, ...)
* `Om_mesh`: :math:`\Omega`-mesh for the optical conductivity. Note that the code repines this mesh to the closest values on the self energy mesh! The new mesh is stored in `Om_meshr`.
The Seebeck coefficient is only calculated if :math:`\Omega=0.0` is included.
* `energy_window`: Limits for the integration over :math:`\omega`. (Due to the Fermi functions the integrand is only of considerable size in a small
window around the Fermi energy.)
* `energy_window`: Limits for the integration over :math:`\omega` (Due to the Fermi functions the integrand is only of considerable size in a small
window around the Fermi energy). For optical conductivity calculations the window is automatically enlarged by :math:`\Omega` .
* `with_Sigma`: If this parameter is set to False then Sigma is set to 0 (i.e. the DFT band structure :math:`A(k,\omega)` is taken).
* `broadening`: The numerical broadening should be set to a finite value for with_Sigma = False.

14
python/converters/wien2k_converter.py
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@ -221,7 +221,7 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
mpi.report("Reading parproj input from %s..."%self.parproj_file)
mpi.report("Reading input from %s..."%self.parproj_file)
dens_mat_below = [ [numpy.zeros([self.shells[ish]['dim'],self.shells[ish]['dim']],numpy.complex_) for ish in range(self.n_shells)]
for isp in range(self.n_spin_blocs) ]
@ -396,7 +396,7 @@ class Wien2kConverter(ConverterTools):
band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in range(SP + 1 - SO)]
for isp, f in enumerate(files):
if not os.path.exists(f): raise IOError, "convert_misc_input: File %s does not exist" %f
print "Reading input from %s..."%f,
mpi.report("Reading input from %s..."%f)
R = ConverterTools.read_fortran_file(self, f, self.fortran_to_replace)
assert int(R.next()) == n_k, "convert_misc_input: Number of k-points is inconsistent in oubwin file!"
@ -416,7 +416,7 @@ class Wien2kConverter(ConverterTools):
# lattice_angles: unit cell angles in rad
if not (os.path.exists(self.struct_file)) : raise IOError, "convert_misc_input: File %s does not exist" %self.struct_file
print "Reading input from %s..."%self.struct_file,
mpi.report("Reading input from %s..."%self.struct_file)
with open(self.struct_file) as R:
try:
@ -434,7 +434,7 @@ class Wien2kConverter(ConverterTools):
# rot_symmetries: matrix representation of all (space group) symmetry operations
if not (os.path.exists(self.outputs_file)) : raise IOError, "convert_misc_input: File %s does not exist" %self.outputs_file
print "Reading input from %s..."%self.outputs_file,
mpi.report("Reading input from %s..."%self.outputs_file)
rot_symmetries = []
with open(self.outputs_file) as R:
@ -499,7 +499,7 @@ class Wien2kConverter(ConverterTools):
band_window_optics = []
for isp, f in enumerate(files):
if not os.path.exists(f) : raise IOError, "convert_transport_input: File %s does not exist" %f
print "Reading input from %s..."%f,
mpi.report("Reading input from %s..."%f)
R = ConverterTools.read_fortran_file(self, f, {'D':'E','(':'',')':'',',':' '})
band_window_optics_isp = []
@ -521,7 +521,7 @@ class Wien2kConverter(ConverterTools):
if (nu_i != nu_j): velocity_xyz[nu_j][nu_i][i] = velocity_xyz[nu_i][nu_j][i].conjugate()
velocities_k[isp].append(velocity_xyz)
band_window_optics.append(numpy.array(band_window_optics_isp))
print "DONE!"
R.close() # Reading done!
# Put data to HDF5 file
ar = HDFArchive(self.hdf_file, 'a')
@ -537,7 +537,7 @@ class Wien2kConverter(ConverterTools):
"""
if not (mpi.is_master_node()): return
mpi.report("Reading symmetry input from %s..."%symm_file)
mpi.report("Reading input from %s..."%symm_file)
n_orbits = len(orbits)

41
python/sumk_dft_tools.py
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@ -480,7 +480,7 @@ class SumkDFTTools(SumkDFT):
return volumecc, volumepc
def transport_distribution(self, directions=['xx'], energy_window=None, Om_mesh=[0.0], beta=40, with_Sigma=False, n_om=None, broadening=0.01):
def transport_distribution(self, directions=['xx'], energy_window=None, Om_mesh=[0.0], beta=40.0, with_Sigma=False, n_om=None, broadening=0.0):
"""
calculate Tr A(k,w) v(k) A(k, w+Om) v(k).
energy_window: regime for omega integral
@ -496,13 +496,16 @@ class SumkDFTTools(SumkDFT):
if not (self.transp_data in ar): raise IOError, "transport_distribution: No %s subgroup in hdf file found! Call convert_transp_input first." %self.transp_data
self.read_transport_input_from_hdf()
if mpi.is_master_node():
# k-dependent-projections.
assert self.k_dep_projection == 1, "transport_distribution: k dependent projection is not implemented!"
# positive Om_mesh
assert all(Om >= 0.0 for Om in Om_mesh), "transport_distribution: Om_mesh should not contain negative values!"
n_inequiv_spin_blocks = self.SP + 1 - self.SO # up and down are equivalent if SP = 0
self.directions = directions
dir_to_int = {'x':0, 'y':1, 'z':2}
dir_to_int = {'x':0, 'y':1, 'z':2}
# k-dependent-projections.
assert self.k_dep_projection == 1, "transport_distribution: k dependent projection is not implemented!"
# calculate A(k,w)
#######################################
@ -515,14 +518,14 @@ class SumkDFTTools(SumkDFT):
print "Using omega mesh provided by Sigma!"
if energy_window is not None:
# Find according window in Sigma mesh
ioffset = numpy.sum(self.omega < energy_window[0])
self.omega = self.omega[numpy.logical_and(self.omega >= energy_window[0], self.omega <= energy_window[1])]
# Find according window in Sigma mesh
ioffset = numpy.sum(self.omega < energy_window[0]-max(Om_mesh))
self.omega = self.omega[numpy.logical_and(self.omega >= energy_window[0]-max(Om_mesh), self.omega <= energy_window[1]+max(Om_mesh))]
n_om = len(self.omega)
# Truncate Sigma to given omega window
# In the future there should be an option in gf to manipulate the mesh (e.g. truncate) directly.
# For we stick with this:
# In the future there should be an option in gf to manipulate the mesh (e.g. truncate) directly.
# For now we stick with this:
for icrsh in range(self.n_corr_shells):
Sigma_save = self.Sigma_imp_w[icrsh].copy()
spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
@ -536,10 +539,10 @@ class SumkDFTTools(SumkDFT):
else:
assert n_om is not None, "transport_distribution: Number of omega points (n_om) needed to calculate transport distribution!"
assert energy_window is not None, "transport_distribution: Energy window needed to calculate transport distribution!"
assert broadening != 0.0 and broadening is not None, "transport_distribution: Broadening necessary to calculate transport distribution!"
self.omega = numpy.linspace(energy_window[0],energy_window[1],n_om)
mesh = [energy_window[0], energy_window[1], n_om]
mu = 0.0
assert broadening != 0.0 and broadening is not None, "transport_distribution: Broadening necessary to calculate transport distribution!"
self.omega = numpy.linspace(energy_window[0]-max(Om_mesh),energy_window[1]+max(Om_mesh),n_om)
mesh = [energy_window[0]-max(Om_mesh), energy_window[1]+max(Om_mesh), n_om]
mu = 0.0
# Check if energy_window is sufficiently large
if (abs(self.fermi_dis(self.omega[0]*beta)*self.fermi_dis(-self.omega[0]*beta)) > 1e-5
@ -550,7 +553,7 @@ class SumkDFTTools(SumkDFT):
# Define mesh for optic conductivity
d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
iOm_mesh = numpy.array([int(Om / d_omega) for Om in Om_mesh])
iOm_mesh = numpy.array([round((Om / d_omega),0) for Om in Om_mesh])
self.Om_mesh = iOm_mesh * d_omega
if mpi.is_master_node():
@ -571,7 +574,7 @@ class SumkDFTTools(SumkDFT):
A_kw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_)
for isp in range(n_inequiv_spin_blocks)]
for isp in range(n_inequiv_spin_blocks):
for isp in range(n_inequiv_spin_blocks):
# Obtain A_kw from G_w (swapaxes is used to have omega in the 3rd dimension)
A_kw[isp].real = -copy.deepcopy(G_w[self.spin_block_names[self.SO][isp]].data.swapaxes(0,1).swapaxes(1,2)).imag / numpy.pi
b_min = max(self.band_window[isp][ik, 0], self.band_window_optics[isp][ik, 0])
@ -588,10 +591,10 @@ class SumkDFTTools(SumkDFT):
vel_R[nu1][nu2][:] = numpy.dot(R, vel_R[nu1][nu2][:])
# calculate Gamma_w for each direction from the velocities vel_R and the spectral function A_kw
for direction in self.directions:
for direction in self.directions:
for iw in xrange(n_om):
for iq in range(len(self.Om_mesh)):
if(iw + iOm_mesh[iq] >= n_om): continue
if(iw + iOm_mesh[iq] >= n_om or self.omega[iw] < -self.Om_mesh[iq] + energy_window[0] or self.omega[iw] > self.Om_mesh[iq] + energy_window[1]): continue
self.Gamma_w[direction][iq, iw] += (numpy.dot(numpy.dot(numpy.dot(vel_R[v_i, v_i, dir_to_int[direction[0]]],
A_kw[isp][A_i, A_i, iw]), vel_R[v_i, v_i, dir_to_int[direction[1]]]),
A_kw[isp][A_i, A_i, iw + iOm_mesh[iq]]).trace().real * self.bz_weights[ik])
@ -649,7 +652,7 @@ class SumkDFTTools(SumkDFT):
if ~numpy.isnan(A1[direction][iq]):
# Seebeck is overwritten if there is more than one Omega = 0 in Om_mesh
self.seebeck[direction] = - A1[direction][iq] / A0[direction][iq] * 86.17
self.optic_cond[direction] = A0[direction] * 10700.0
self.optic_cond[direction] = beta * A0[direction] * 10700.0 / numpy.pi
for iq in xrange(n_q):
print "Conductivity in direction %s for Omega = %.2f %f x 10^4 Ohm^-1 cm^-1" % (direction, self.Om_mesh[iq], self.optic_cond[direction][iq])
if not (numpy.isnan(A1[direction][iq])):

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test/SrVO3.h5
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test/srvo3_transp.output.h5
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