mirror of
https://github.com/triqs/dft_tools
synced 2024-06-26 07:02:19 +02:00
Restore everything which was lost in rebase.
This commit is contained in:
Manuel Zingl
parent
fd7ab682a4
commit
b3b199bf40
|
|
@ -54,7 +54,7 @@ class Wien2kConverter(ConverterTools):
|
|||
self.bands_subgrp = bands_subgrp
|
||||
self.transp_subgrp = transp_subgrp
|
||||
self.fortran_to_replace = {'D':'E'}
|
||||
self.vel_file = filename+'.pmat'
|
||||
self.pmat_file = filename+'.pmat'
|
||||
self.outputs_file = filename+'.outputs'
|
||||
self.struct_file = filename+'.struct'
|
||||
self.oubwin_file = filename+'.oubwin'
|
||||
|
|
@ -373,166 +373,137 @@ class Wien2kConverter(ConverterTools):
|
|||
Reads the input files necessary for transport calculations
|
||||
and stores the data in the HDFfile
|
||||
"""
|
||||
|
||||
#Read and write files only on the master node
|
||||
if not (mpi.is_master_node()): return
|
||||
|
||||
# Check if SP, SO and n_k are already in h5
|
||||
ar = HDFArchive(self.hdf_file, 'a')
|
||||
if not (self.dft_subgrp in ar): raise IOError, "No %s subgroup in hdf file found! Call convert_dmft_input first." %self.dft_subgrp
|
||||
if not (self.dft_subgrp in ar): raise IOError, "convert_transport_input: No %s subgroup in hdf file found! Call convert_dmft_input first." %self.dft_subgrp
|
||||
SP = ar[self.dft_subgrp]['SP']
|
||||
SO = ar[self.dft_subgrp]['SO']
|
||||
n_k = ar[self.dft_subgrp]['n_k']
|
||||
del ar
|
||||
|
||||
# Read relevant data from .pmat file
|
||||
############################################
|
||||
|
||||
# Read relevant data from .pmat/up/dn files
|
||||
###########################################
|
||||
# band_window_optics: Contains the index of the lowest and highest band within the
|
||||
# band window (used by optics) for each k-point.
|
||||
# velocities_k: velocity (momentum) matrix elements between all bands in band_window_optics
|
||||
# and each k-point.
|
||||
|
||||
if (SP == 0 or SO == 1):
|
||||
files = [self.vel_file]
|
||||
files = [self.pmat_file]
|
||||
elif SP == 1:
|
||||
files = [self.vel_file+'up', self.vel_file+'dn']
|
||||
files = [self.pmat_file+'up', self.pmat_file+'dn']
|
||||
else: # SO and SP can't both be 1
|
||||
assert 0, "convert_transport_input: reading velocity file error! Check SP and SO!"
|
||||
assert 0, "convert_transport_input: Reading velocity file error! Check SP and SO!"
|
||||
|
||||
vk = [[] for f in files]
|
||||
kp = [[] for f in files]
|
||||
bandwin_opt = []
|
||||
|
||||
velocities_k = [[] for f in files]
|
||||
band_window_optics = []
|
||||
for isp, f in enumerate(files):
|
||||
bandwin_opt_isp = []
|
||||
if not os.path.exists(f) : raise IOError, "File %s does not exist" %f
|
||||
print "Reading input from %s..."%f
|
||||
|
||||
with open(f) as R:
|
||||
while 1:
|
||||
try:
|
||||
s = R.readline()
|
||||
if (s == ''):
|
||||
break
|
||||
except:
|
||||
break
|
||||
try:
|
||||
[k, nu1, nu2] = [int(x) for x in s.strip().split()]
|
||||
bandwin_opt_isp.append((nu1,nu2))
|
||||
dim = nu2 - nu1 +1
|
||||
v_xyz = numpy.zeros((dim,dim,3), dtype = complex)
|
||||
temp = R.readline().strip().split()
|
||||
kp[isp].append(numpy.array([float(t) for t in temp[0:3]]))
|
||||
for nu_i in xrange(dim):
|
||||
for nu_j in xrange(nu_i, dim):
|
||||
for i in xrange(3):
|
||||
s = R.readline().strip("\n ()").split(',')
|
||||
v_xyz[nu_i][nu_j][i] = float(s[0]) + float(s[1])*1j
|
||||
if (nu_i != nu_j):
|
||||
v_xyz[nu_j][nu_i][i] = v_xyz[nu_i][nu_j][i].conjugate()
|
||||
|
||||
vk[isp].append(v_xyz)
|
||||
|
||||
except IOError:
|
||||
raise "Wien2k_converter : reading file %s failed" %self.vel_file
|
||||
bandwin_opt.append(numpy.array(bandwin_opt_isp))
|
||||
|
||||
print "Read in %s file done!" %self.vel_file
|
||||
if not os.path.exists(f) : raise IOError, "convert_transport_input: File %s does not exist" %f
|
||||
print "Reading input from %s..."%f,
|
||||
|
||||
R = ConverterTools.read_fortran_file(self, f, {'D':'E','(':'',')':'',',':''})
|
||||
band_window_optics_isp = []
|
||||
for ik in xrange(n_k):
|
||||
R.next()
|
||||
nu1 = int(R.next())
|
||||
nu2 = int(R.next())
|
||||
band_window_optics_isp.append((nu1, nu2))
|
||||
n_bands = nu2 - nu1 + 1
|
||||
velocity_xyz = numpy.zeros((n_bands, n_bands, 3), dtype = complex)
|
||||
for _ in range(4): R.next()
|
||||
for nu_i in range(n_bands):
|
||||
for nu_j in range(nu_i, n_bands):
|
||||
for i in range(3):
|
||||
velocity_xyz[nu_i][nu_j][i] = R.next() + R.next()*1j
|
||||
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!"
|
||||
|
||||
# Read relevant data from .struct file
|
||||
############################################
|
||||
if not (os.path.exists(self.struct_file)) : raise IOError, "File %s does not exist" %self.struct_file
|
||||
print "Reading input from %s..."%self.struct_file
|
||||
######################################
|
||||
# lattice_type: bravais lattice type as defined by Wien2k
|
||||
# lattice_constants: unit cell parameters in a. u.
|
||||
# lattice_angles: unit cell angles in rad
|
||||
|
||||
if not (os.path.exists(self.struct_file)) : raise IOError, "convert_transport_input: File %s does not exist" %self.struct_file
|
||||
print "Reading input from %s..."%self.struct_file,
|
||||
|
||||
with open(self.struct_file) as f:
|
||||
with open(self.struct_file) as R:
|
||||
try:
|
||||
f.readline() #title
|
||||
temp = f.readline() #lattice
|
||||
latticetype = temp.split()[0]
|
||||
f.readline()
|
||||
temp = f.readline().strip().split() # lattice constants
|
||||
latticeconstants = numpy.array([float(t) for t in temp[0:3]])
|
||||
latticeangles = numpy.array([float(t) for t in temp[3:6]])
|
||||
latticeangles *= numpy.pi/180.0
|
||||
print 'Lattice: ', latticetype
|
||||
print 'Lattice constants: ', latticeconstants
|
||||
print 'Lattice angles: ', latticeangles
|
||||
|
||||
R.readline()
|
||||
lattice_type = R.readline().split()[0]
|
||||
R.readline()
|
||||
temp = R.readline().strip().split()
|
||||
lattice_constants = numpy.array([float(t) for t in temp[0:3]])
|
||||
lattice_angles = numpy.array([float(t) for t in temp[3:6]]) * numpy.pi / 180.0
|
||||
except IOError:
|
||||
raise "Wien2k_converter : reading file %s failed" %self.struct_file
|
||||
|
||||
print "Read in %s file done!" %self.struct_file
|
||||
|
||||
raise "convert_transport_input: reading file %s failed" %self.struct_file
|
||||
print "DONE!"
|
||||
|
||||
# Read relevant data from .outputs file
|
||||
############################################
|
||||
if not (os.path.exists(self.outputs_file)) : raise IOError, "File %s does not exist" %self.outputs_file
|
||||
print "Reading input from %s..."%self.outputs_file
|
||||
#######################################
|
||||
# rot_symmetries: matrix representation of all (space group) symmetry operations
|
||||
|
||||
symmcartesian = []
|
||||
taucartesian = []
|
||||
|
||||
with open(self.outputs_file) as f:
|
||||
if not (os.path.exists(self.outputs_file)) : raise IOError, "convert_transport_input: File %s does not exist" %self.outputs_file
|
||||
print "Reading input from %s..."%self.outputs_file,
|
||||
|
||||
rot_symmetries = []
|
||||
with open(self.outputs_file) as R:
|
||||
try:
|
||||
while 1:
|
||||
temp = f.readline().strip(' ').split()
|
||||
temp = R.readline().strip(' ').split()
|
||||
if (temp[0] =='PGBSYM:'):
|
||||
nsymm = int(temp[-1])
|
||||
n_symmetries = int(temp[-1])
|
||||
break
|
||||
for i in range(nsymm):
|
||||
for i in range(n_symmetries):
|
||||
while 1:
|
||||
temp = f.readline().strip().split()
|
||||
if (temp[0] == 'Symmetry'):
|
||||
break
|
||||
|
||||
# read cartesian symmetries
|
||||
symmt = numpy.zeros((3, 3), dtype = float)
|
||||
taut = numpy.zeros(3, dtype = float)
|
||||
if (R.readline().strip().split()[0] == 'Symmetry'): break
|
||||
sym_i = numpy.zeros((3, 3), dtype = float)
|
||||
for ir in range(3):
|
||||
temp = f.readline().strip().split()
|
||||
temp = R.readline().strip().split()
|
||||
for ic in range(3):
|
||||
symmt[ir, ic] = float(temp[ic])
|
||||
temp = f.readline().strip().split()
|
||||
for ir in range(3):
|
||||
taut[ir] = float(temp[ir])
|
||||
|
||||
symmcartesian.append(symmt)
|
||||
taucartesian.append(taut)
|
||||
sym_i[ir, ic] = float(temp[ic])
|
||||
R.readline()
|
||||
rot_symmetries.append(sym_i)
|
||||
except IOError:
|
||||
raise "Wien2k_converter: reading file %s failed" %self.outputs_file
|
||||
|
||||
print "Read in %s file done!" %self.outputs_file
|
||||
raise "convert_transport_input: reading file %s failed" %self.outputs_file
|
||||
print "DONE!"
|
||||
|
||||
|
||||
# Read relevant data from .oubwin/up/down files
|
||||
############################################
|
||||
# Read relevant data from .oubwin/up/dn files
|
||||
###############################################
|
||||
# band_window: Contains the index of the lowest and highest band within the
|
||||
# projected subspace (used by dmftproj) for each k-point.
|
||||
|
||||
if (SP == 0 or SO == 1):
|
||||
files = [self.oubwin_file]
|
||||
elif SP == 1:
|
||||
files = [self.oubwin_file+'up', self.oubwin_file+'dn']
|
||||
else: # SO and SP can't both be 1
|
||||
assert 0, "Reding oubwin error! Check SP and SO!"
|
||||
bandwin = [numpy.zeros((n_k, 2), dtype=int) for isp in range(SP + 1 - SO)]
|
||||
|
||||
assert 0, "convert_transport_input: Reding oubwin error! Check SP and SO!"
|
||||
|
||||
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, "File %s does not exist" %f
|
||||
print "Reading input from %s..."%f
|
||||
if not os.path.exists(f): raise IOError, "convert_transport_input: File %s does not exist" %f
|
||||
print "Reading input from %s..."%f,
|
||||
|
||||
R = ConverterTools.read_fortran_file(self, f, self.fortran_to_replace)
|
||||
assert int(R.next()) == n_k, "Wien2k_converter: Number of k-points is inconsistent in oubwin file!"
|
||||
assert int(R.next()) == SO, "Wien2k_converter: SO is inconsistent in oubwin file!"
|
||||
|
||||
assert int(R.next()) == n_k, "convert_transport_input: Number of k-points is inconsistent in oubwin file!"
|
||||
assert int(R.next()) == SO, "convert_transport_input: SO is inconsistent in oubwin file!"
|
||||
for ik in xrange(n_k):
|
||||
R.next()
|
||||
bandwin[isp][ik,0] = R.next()
|
||||
bandwin[isp][ik,1] = R.next()
|
||||
band_window[isp][ik,0] = R.next()
|
||||
band_window[isp][ik,1] = R.next()
|
||||
R.next()
|
||||
|
||||
print "Read in %s files done!" %self.oubwin_file
|
||||
print "DONE!"
|
||||
|
||||
# Put data to HDF5 file
|
||||
ar = HDFArchive(self.hdf_file, 'a')
|
||||
if not (self.transp_subgrp in ar): ar.create_group(self.transp_subgrp)
|
||||
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!!!
|
||||
things_to_save = ['bandwin', 'bandwin_opt', 'kp', 'vk', 'latticetype', 'latticeconstants', 'latticeangles', 'nsymm', 'symmcartesian',
|
||||
'taucartesian']
|
||||
things_to_save = ['band_window', 'band_window_optics', 'velocities_k', 'lattice_type', 'lattice_constants', 'lattice_angles', 'n_symmetries', 'rot_symmetries']
|
||||
for it in things_to_save: ar[self.transp_subgrp][it] = locals()[it]
|
||||
del ar
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,3 @@
|
|||
|
||||
################################################################################
|
||||
#
|
||||
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
|
||||
|
|
@ -501,72 +500,72 @@ class SumkDFTTools(SumkDFT):
|
|||
"""
|
||||
Reads the data for transport calculations from the HDF file
|
||||
"""
|
||||
|
||||
thingstoread = ['bandwin','bandwin_opt','kp','latticeangles','latticeconstants','latticetype','nsymm','symmcartesian','vk']
|
||||
thingstoread = ['band_window','band_window_optics','velocities_k','lattice_angles','lattice_constants','lattice_type','n_symmetries','rot_symmetries']
|
||||
retval = self.read_input_from_hdf(subgrp=self.transp_data,things_to_read = thingstoread)
|
||||
return retval
|
||||
|
||||
|
||||
def cellvolume(self, latticetype, latticeconstants, latticeangle):
|
||||
def cellvolume(self, lattice_type, lattice_constants, latticeangle):
|
||||
"""
|
||||
Calculate cell volume: volumecc conventional cell, volumepc, primitive cell.
|
||||
"""
|
||||
a = latticeconstants[0]
|
||||
b = latticeconstants[1]
|
||||
c = latticeconstants[2]
|
||||
a = lattice_constants[0]
|
||||
b = lattice_constants[1]
|
||||
c = lattice_constants[2]
|
||||
c_al = numpy.cos(latticeangle[0])
|
||||
c_be = numpy.cos(latticeangle[1])
|
||||
c_ga = numpy.cos(latticeangle[2])
|
||||
volumecc = a * b * c * numpy.sqrt(1 + 2 * c_al * c_be * c_ga - c_al ** 2 - c_be * 82 - c_ga ** 2)
|
||||
|
||||
det = {"P":1, "F":4, "B":2, "R":3, "H":1, "CXY":2, "CYZ":2, "CXZ":2}
|
||||
volumepc = volumecc / det[latticetype]
|
||||
volumepc = volumecc / det[lattice_type]
|
||||
|
||||
return volumecc, volumepc
|
||||
|
||||
|
||||
def transport_distribution(self, dir_list=[(0,0)], broadening=0.01, energywindow=None, Om_mesh=[0.0], beta=40, with_Sigma=False, n_om=None):
|
||||
"""calculate Tr A(k,w) v(k) A(k, w+q) v(k) and optics.
|
||||
energywindow: regime for omega integral
|
||||
Om_mesh: contains the frequencies of the optic conductivitity. Om_mesh is repinned to the self-energy mesh
|
||||
(hence exact values might be different from those given in Om_mesh)
|
||||
dir_list: list to defines the indices of directions. xx,yy,zz,xy,yz,zx.
|
||||
((0, 0) --> xx, (1, 1) --> yy, (0, 2) --> xz, default: (0, 0))
|
||||
with_Sigma: Use Sigma = 0 if False
|
||||
def transport_distribution(self, directions=['xx'], energy_window=None, Om_mesh=[0.0], beta=40, with_Sigma=False, n_om=None, broadening=0.01):
|
||||
"""
|
||||
calculate Tr A(k,w) v(k) A(k, w+Om) v(k).
|
||||
energy_window: regime for omega integral
|
||||
Om_mesh: mesh for optic conductivitity. Om_mesh is repinned to the self-energy mesh!
|
||||
directions: list of directions: xx,yy,zz,xy,yz,zx.
|
||||
with_Sigma: Use Sigma_w = 0 if False (In this case it is necessary to specifiy the energywindow (energy_window),
|
||||
the number of omega points (n_om) in the window and the broadening (broadening)).
|
||||
"""
|
||||
|
||||
# Check if wien converter was called
|
||||
# Check if wien converter was called and read transport subgroup form hdf file
|
||||
if mpi.is_master_node():
|
||||
ar = HDFArchive(self.hdf_file, 'a')
|
||||
if not (self.transp_data in ar): raise IOError, "No %s subgroup in hdf file found! Call convert_transp_input first." %self.transp_data
|
||||
|
||||
self.dir_list = dir_list
|
||||
|
||||
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()
|
||||
velocities = self.vk
|
||||
n_inequiv_spin_blocks = self.SP + 1 - self.SO # up and down are equivalent if SP = 0
|
||||
|
||||
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}
|
||||
|
||||
# k-dependent-projections.
|
||||
assert self.k_dep_projection == 1, "transport_distribution: k dependent projection is not implemented!"
|
||||
|
||||
# calculate A(k,w)
|
||||
#######################################
|
||||
|
||||
# use k-dependent-projections.
|
||||
assert self.k_dep_projection == 1, "Not implemented!"
|
||||
|
||||
# Define mesh for Greens function and the used energy range
|
||||
# Define mesh for Greens function and in the specified energy window
|
||||
if (with_Sigma == True):
|
||||
self.omega = numpy.array([round(x.real,12) for x in self.Sigma_imp_w[0].mesh])
|
||||
mesh = None
|
||||
mu = self.chemical_potential
|
||||
n_om = len(self.omega)
|
||||
print "Using omega mesh provided by Sigma."
|
||||
print "Using omega mesh provided by Sigma!"
|
||||
|
||||
if energywindow is not None:
|
||||
# Find according window in Sigma mesh
|
||||
ioffset = numpy.sum(self.omega < energywindow[0])
|
||||
self.omega = self.omega[numpy.logical_and(self.omega >= energywindow[0], self.omega <= energywindow[1])]
|
||||
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])]
|
||||
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:
|
||||
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']]
|
||||
|
|
@ -576,179 +575,133 @@ class SumkDFTTools(SumkDFT):
|
|||
for iL in g.indices:
|
||||
for iR in g.indices:
|
||||
for iom in xrange(n_om):
|
||||
g.data[iom,iL,iR] = Sigma_save[i].data[ioffset+iom,iL,iR] # FIXME IS THIS CLEAN? MANIPULATING data DIRECTLY?
|
||||
|
||||
g.data[iom,iL,iR] = Sigma_save[i].data[ioffset+iom,iL,iR]
|
||||
else:
|
||||
assert n_om is not None, "Number of omega points (n_om) needed!"
|
||||
assert energywindow is not None, "Energy window needed!"
|
||||
self.omega = numpy.linspace(energywindow[0],energywindow[1],n_om)
|
||||
mu = 0.0
|
||||
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
|
||||
|
||||
# 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
|
||||
or abs(self.fermi_dis(self.omega[-1]*beta)*self.fermi_dis(-self.omega[-1]*beta)) > 1e-5):
|
||||
print "\n##########################################"
|
||||
print "WARNING: Energywindow might be too narrow!"
|
||||
print "##########################################\n"
|
||||
print "\n####################################################################"
|
||||
print "transport_distribution: WARNING - energy window might be too narrow!"
|
||||
print "####################################################################\n"
|
||||
|
||||
# Define mesh for optic conductivity
|
||||
d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
|
||||
|
||||
# define exact mesh for optic conductivity
|
||||
Om_mesh_ex = numpy.array([int(x / d_omega) for x in Om_mesh])
|
||||
self.Om_meshr= Om_mesh_ex*d_omega
|
||||
iOm_mesh = numpy.array([int(Om / d_omega) for Om in Om_mesh])
|
||||
self.Om_mesh = iOm_mesh * d_omega
|
||||
|
||||
if mpi.is_master_node():
|
||||
print "Chemical potential: ", mu
|
||||
print "Using n_om = %s points in the energywindow [%s,%s]"%(n_om, self.omega[0], self.omega[-1])
|
||||
print "omega vector is:"
|
||||
print "Using n_om = %s points in the energy_window [%s,%s]"%(n_om, self.omega[0], self.omega[-1]),
|
||||
print "where the omega vector is:"
|
||||
print self.omega
|
||||
print "Omega mesh interval ", d_omega
|
||||
print "Provided Om_mesh ", numpy.array(Om_mesh)
|
||||
print "Pinnend Om_mesh to ", self.Om_meshr
|
||||
print "Calculation requested for Omega mesh: ", numpy.array(Om_mesh)
|
||||
print "Omega mesh automatically repinned to: ", self.Om_mesh
|
||||
|
||||
# output P(\omega)_xy should have the same dimension as defined in mshape.
|
||||
self.Pw_optic = numpy.zeros((len(dir_list), len(Om_mesh_ex), n_om), dtype=numpy.float_)
|
||||
|
||||
ik = 0
|
||||
|
||||
spn = self.spin_block_names[self.SO]
|
||||
ntoi = self.spin_names_to_ind[self.SO]
|
||||
|
||||
G_w = BlockGf(name_block_generator=[(spn[isp], GfReFreq(indices=range(self.n_orbitals[ik][isp]), window=(self.omega[0], self.omega[-1]), n_points = n_om))
|
||||
for isp in range(n_inequiv_spin_blocks) ], make_copies=False)
|
||||
mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(n_inequiv_spin_blocks)] # construct mupat
|
||||
Annkw = [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)]
|
||||
self.Gamma_w = {direction: numpy.zeros((len(self.Om_mesh), n_om), dtype=numpy.float_) for direction in self.directions}
|
||||
|
||||
# Sum over all k-points
|
||||
ikarray = numpy.array(range(self.n_k))
|
||||
for ik in mpi.slice_array(ikarray):
|
||||
unchangedsize = all([ self.n_orbitals[ik][isp] == mupat[isp].shape[0] for isp in range(n_inequiv_spin_blocks)])
|
||||
if not unchangedsize:
|
||||
# recontruct green functions.
|
||||
G_w = BlockGf(name_block_generator=[(spn[isp], GfReFreq(indices=range(self.n_orbitals[ik][isp]), window = (self.omega[0], self.omega[-1]), n_points = n_om))
|
||||
for isp in range(n_inequiv_spin_blocks) ], make_copies=False)
|
||||
# construct mupat
|
||||
mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(n_inequiv_spin_blocks)]
|
||||
#set a temporary array storing spectral functions with band index. Note, usually we should have spin index
|
||||
Annkw = [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)]
|
||||
# get lattice green function
|
||||
# Calculate G_w for ik and initialize A_kw
|
||||
G_w = self.lattice_gf(ik, mu, iw_or_w="w", beta=beta, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma)
|
||||
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)]
|
||||
|
||||
G_w << 1*Omega + 1j*broadening
|
||||
|
||||
MS = copy.deepcopy(mupat)
|
||||
for ibl in range(n_inequiv_spin_blocks):
|
||||
ind = ntoi[spn[ibl]]
|
||||
n_orb = self.n_orbitals[ik][ibl]
|
||||
MS[ibl] = self.hopping[ik,ind,0:n_orb,0:n_orb].real - mupat[ibl]
|
||||
G_w -= MS
|
||||
|
||||
if (with_Sigma == True):
|
||||
tmp = G_w.copy() # init temporary storage
|
||||
# form self energy from impurity self energy and double counting term.
|
||||
sigma_minus_dc = self.add_dc(iw_or_w="w")
|
||||
# substract self energy
|
||||
for icrsh in range(self.n_corr_shells):
|
||||
for sig, gf in tmp: tmp[sig] << self.upfold(ik, icrsh, sig, sigma_minus_dc[icrsh][sig], gf)
|
||||
G_w -= tmp
|
||||
|
||||
G_w.invert()
|
||||
|
||||
for isp in range(n_inequiv_spin_blocks):
|
||||
Annkw[isp].real = -copy.deepcopy(G_w[self.spin_block_names[self.SO][isp]].data.swapaxes(0,1).swapaxes(1,2)).imag / numpy.pi
|
||||
|
||||
for isp in range(n_inequiv_spin_blocks):
|
||||
kvel = velocities[isp][ik]
|
||||
Pwtem = numpy.zeros((len(dir_list), len(Om_mesh_ex), n_om), dtype=numpy.float_)
|
||||
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])
|
||||
b_max = min(self.band_window[isp][ik, 1], self.band_window_optics[isp][ik, 1])
|
||||
A_i = slice(b_min - self.band_window[isp][ik, 0], b_max - self.band_window[isp][ik, 0] + 1)
|
||||
v_i = slice(b_min - self.band_window_optics[isp][ik, 0], b_max - self.band_window_optics[isp][ik, 0] + 1)
|
||||
|
||||
bmin = max(self.bandwin[isp][ik, 0], self.bandwin_opt[isp][ik, 0])
|
||||
bmax = min(self.bandwin[isp][ik, 1], self.bandwin_opt[isp][ik, 1])
|
||||
Astart = bmin - self.bandwin[isp][ik, 0]
|
||||
Aend = bmax - self.bandwin[isp][ik, 0] + 1
|
||||
vstart = bmin - self.bandwin_opt[isp][ik, 0]
|
||||
vend = bmax - self.bandwin_opt[isp][ik, 0] + 1
|
||||
|
||||
#symmetry loop
|
||||
for Rmat in self.symmcartesian:
|
||||
# get new velocity.
|
||||
Rkvel = copy.deepcopy(kvel)
|
||||
for vnb1 in range(self.bandwin_opt[isp][ik, 1] - self.bandwin_opt[isp][ik, 0] + 1):
|
||||
for vnb2 in range(self.bandwin_opt[isp][ik, 1] - self.bandwin_opt[isp][ik, 0] + 1):
|
||||
Rkvel[vnb1][vnb2][:] = numpy.dot(Rmat, Rkvel[vnb1][vnb2][:])
|
||||
ipw = 0
|
||||
for (ir, ic) in dir_list:
|
||||
# loop over all symmetries
|
||||
for R in self.rot_symmetries:
|
||||
# get transformed velocity under symmetry R
|
||||
vel_R = copy.deepcopy(self.velocities_k[isp][ik])
|
||||
for nu1 in range(self.band_window_optics[isp][ik, 1] - self.band_window_optics[isp][ik, 0] + 1):
|
||||
for nu2 in range(self.band_window_optics[isp][ik, 1] - self.band_window_optics[isp][ik, 0] + 1):
|
||||
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 iw in xrange(n_om):
|
||||
for iq in range(len(Om_mesh_ex)):
|
||||
if(iw + Om_mesh_ex[iq] >= n_om):
|
||||
continue
|
||||
|
||||
# construct matrix for A and velocity.
|
||||
Annkwl = Annkw[isp][Astart:Aend, Astart:Aend, iw]
|
||||
Annkwr = Annkw[isp][Astart:Aend, Astart:Aend, iw + Om_mesh_ex[iq]]
|
||||
Rkveltr = Rkvel[vstart:vend, vstart:vend, ir]
|
||||
Rkveltc = Rkvel[vstart:vend, vstart:vend, ic]
|
||||
# print Annkwl.shape, Annkwr.shape, Rkveltr.shape, Rkveltc.shape
|
||||
Pwtem[ipw, iq, iw] += numpy.dot(numpy.dot(numpy.dot(Rkveltr, Annkwl), Rkveltc), Annkwr).trace().real
|
||||
ipw += 1
|
||||
|
||||
# k sum and spin sum.
|
||||
self.Pw_optic += Pwtem * self.bz_weights[ik] / self.nsymm
|
||||
|
||||
self.Pw_optic = mpi.all_reduce(mpi.world, self.Pw_optic, lambda x, y : x + y)
|
||||
self.Pw_optic *= (2 - self.SP)
|
||||
for iq in range(len(self.Om_mesh)):
|
||||
if(iw + iOm_mesh[iq] >= n_om): 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])
|
||||
|
||||
for direction in self.directions:
|
||||
self.Gamma_w[direction] = (mpi.all_reduce(mpi.world, self.Gamma_w[direction], lambda x, y : x + y)
|
||||
/ self.cellvolume(self.lattice_type, self.lattice_constants, self.lattice_angles)[1]) / self.n_symmetries
|
||||
|
||||
def conductivity_and_seebeck(self, beta=40):
|
||||
""" #return 1/T*A0, that is Conductivity in unit 1/V
|
||||
calculate, save and return Conductivity
|
||||
|
||||
def transport_coefficient(self, direction, iq=0, n=0, beta=40):
|
||||
"""
|
||||
calculates the transport coefficients A_n in a given direction and for a given Omega. (see documentation)
|
||||
A_1 is set to nan if requested for Omega != 0.0
|
||||
iq: index of Omega point in Om_mesh
|
||||
direction: 'xx','yy','zz','xy','xz','yz'
|
||||
"""
|
||||
if not (mpi.is_master_node()): return
|
||||
|
||||
assert hasattr(self,'Gamma_w'), "transport_coefficient: Run transport_distribution first or load data from h5!"
|
||||
A = 0.0
|
||||
omegaT = self.omega * beta
|
||||
d_omega = self.omega[1] - self.omega[0]
|
||||
if (self.Om_mesh[iq] == 0.0):
|
||||
for iw in xrange(self.Gamma_w[direction].shape[1]):
|
||||
A += self.Gamma_w[direction][iq, iw] * self.fermi_dis(omegaT[iw]) * self.fermi_dis(-omegaT[iw]) * numpy.float(omegaT[iw])**n * d_omega
|
||||
elif (n == 0.0):
|
||||
for iw in xrange(self.Gamma_w[direction].shape[1]):
|
||||
A += (self.Gamma_w[direction][iq, iw] * (self.fermi_dis(omegaT[iw]) - self.fermi_dis(omegaT[iw] + self.Om_mesh[iq] * beta))
|
||||
/ (self.Om_mesh[iq] * beta) * d_omega)
|
||||
else:
|
||||
A = numpy.nan
|
||||
return A * numpy.pi * (2.0-self.SP)
|
||||
|
||||
if mpi.is_master_node():
|
||||
assert hasattr(self,'Pw_optic'), "Run transport_distribution first or load data from h5!"
|
||||
assert hasattr(self,'latticetype'), "Run convert_transp_input first or load data from h5!"
|
||||
|
||||
volcc, volpc = self.cellvolume(self.latticetype, self.latticeconstants, self.latticeangles)
|
||||
|
||||
n_direction, n_q, n_w= self.Pw_optic.shape
|
||||
omegaT = self.omega * beta
|
||||
A0 = numpy.zeros((n_direction,n_q), dtype=numpy.float_)
|
||||
q_0 = False
|
||||
self.seebeck = numpy.zeros((n_direction,), dtype=numpy.float_)
|
||||
self.seebeck[:] = numpy.NAN
|
||||
|
||||
d_omega = self.omega[1] - self.omega[0]
|
||||
for iq in xrange(n_q):
|
||||
# treat q = 0, caclulate conductivity and seebeck
|
||||
if (self.Om_meshr[iq] == 0.0):
|
||||
# if Om_meshr contains multiple entries with w=0, A1 is overwritten!
|
||||
q_0 = True
|
||||
A1 = numpy.zeros((n_direction,), dtype=numpy.float_)
|
||||
for idir in range(n_direction):
|
||||
for iw in xrange(n_w):
|
||||
A0[idir, iq] += beta * self.Pw_optic[idir, iq, iw] * self.fermi_dis(omegaT[iw]) * self.fermi_dis(-omegaT[iw])
|
||||
A1[idir] += beta * self.Pw_optic[idir, iq, iw] * self.fermi_dis(omegaT[iw]) * self.fermi_dis(-omegaT[iw]) * numpy.float(omegaT[iw])
|
||||
self.seebeck[idir] = -A1[idir] / A0[idir, iq]
|
||||
print "A0", A0[idir, iq] *d_omega/beta
|
||||
print "A1", A1[idir] *d_omega/beta
|
||||
# treat q ~= 0, calculate optical conductivity
|
||||
else:
|
||||
for idir in range(n_direction):
|
||||
for iw in xrange(n_w):
|
||||
A0[idir, iq] += self.Pw_optic[idir, iq, iw] * (self.fermi_dis(omegaT[iw]) - self.fermi_dis(omegaT[iw] + self.Om_meshr[iq] * beta)) / self.Om_meshr[iq]
|
||||
|
||||
A0 *= d_omega
|
||||
#cond = beta * self.tdintegral(beta, 0)[index]
|
||||
print "V in bohr^3 ", volpc
|
||||
# transform to standard unit as in resistivity
|
||||
self.optic_cond = A0 * 10700.0 / volpc
|
||||
self.seebeck *= 86.17
|
||||
|
||||
# print
|
||||
for im in range(n_direction):
|
||||
for iq in xrange(n_q):
|
||||
print "Conductivity in direction %s for Om_mesh %d %.4f x 10^4 Ohm^-1 cm^-1" % (self.dir_list[im], iq, self.optic_cond[im, iq])
|
||||
print "Resistivity in direction %s for Om_mesh %d %.4f x 10^-4 Ohm cm" % (self.dir_list[im], iq, 1.0 / self.optic_cond[im, iq])
|
||||
if q_0:
|
||||
print "Seebeck in direction %s for q = 0 %.4f x 10^(-6) V/K" % (self.dir_list[im], self.seebeck[im])
|
||||
|
||||
|
||||
def conductivity_and_seebeck(self, beta=40):
|
||||
"""
|
||||
Calculates the Seebeck coefficient and the conductivity for a given Gamma_w
|
||||
"""
|
||||
if not (mpi.is_master_node()): return
|
||||
|
||||
assert hasattr(self,'Gamma_w'), "conductivity_and_seebeck: Run transport_distribution first or load data from h5!"
|
||||
n_q = self.Gamma_w[self.directions[0]].shape[0]
|
||||
|
||||
A0 = {direction: numpy.full((n_q,),numpy.nan) for direction in self.directions}
|
||||
A1 = {direction: numpy.full((n_q,),numpy.nan) for direction in self.directions}
|
||||
self.seebeck = {direction: numpy.nan for direction in self.directions}
|
||||
self.optic_cond = {direction: numpy.full((n_q,),numpy.nan) for direction in self.directions}
|
||||
|
||||
for direction in self.directions:
|
||||
for iq in xrange(n_q):
|
||||
A0[direction][iq] = self.transport_coefficient(direction, iq=iq, n=0, beta=beta)
|
||||
A1[direction][iq] = self.transport_coefficient(direction, iq=iq, n=1, beta=beta)
|
||||
print "A_0 in direction %s for Omega = %.2f %e a.u." % (direction, self.Om_mesh[iq], A0[direction][iq])
|
||||
print "A_1 in direction %s for Omega = %.2f %e a.u." % (direction, self.Om_mesh[iq], A1[direction][iq])
|
||||
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
|
||||
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])):
|
||||
print "Seebeck in direction %s for Omega = 0.00 %f x 10^(-6) V/K" % (direction, self.seebeck[direction])
|
||||
|
||||
|
||||
def fermi_dis(self, x):
|
||||
"""
|
||||
fermi distribution at x = omega * beta
|
||||
"""
|
||||
return 1.0/(numpy.exp(x)+1)
|
||||
|
||||
|
|
|
|||
BIN
test/SrVO3.h5
BIN
test/SrVO3.h5
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
|
@ -33,13 +33,13 @@ Converter.convert_transport_input()
|
|||
SK = SumkDFTTools(hdf_file='SrVO3.h5', use_dft_blocks=True)
|
||||
|
||||
ar = HDFArchive('SrVO3_Sigma.h5', 'a')
|
||||
Sigma = ar['dmft_transp_output']['Sigma']
|
||||
Sigma = ar['dmft_transp_output']['Sigma_w']
|
||||
SK.put_Sigma(Sigma_imp = [Sigma])
|
||||
del ar
|
||||
|
||||
SK.transport_distribution(dir_list=[(0,0)], broadening=0.0, energywindow=[-0.3,0.3], Om_mesh=[0.00, 0.02] , beta=beta, with_Sigma=True)
|
||||
#SK.save(['Pw_optic','Om_meshr','omega','dir_list'])
|
||||
#SK.load(['Pw_optic','Om_meshr','omega','dir_list'])
|
||||
SK.transport_distribution(directions=['xx'], broadening=0.0, energy_window=[-0.3,0.3], Om_mesh=[0.00, 0.02] , beta=beta, with_Sigma=True)
|
||||
#SK.save(['Gamma_w','Om_meshr','omega','directions'])
|
||||
#SK.load(['Gamma_w','Om_meshr','omega','directions'])
|
||||
SK.conductivity_and_seebeck(beta=beta)
|
||||
SK.hdf_file = 'srvo3_transp.output.h5'
|
||||
SK.save(['seebeck','optic_cond'])
|
||||
|
|
|
|||
Loading…
Reference in New Issue
Block a user