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https://github.com/triqs/dft_tools
synced 2024-12-21 11:53:41 +01:00
Fix error in transport code, some modifications
This commit is contained in:
Manuel Zingl
parent
674059506f
commit
373764f680
@ -85,10 +85,12 @@ First we have to read the Wien2k files and store the relevant information in the
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SK = SumkDFTTools(hdf_file='case.h5', use_dft_blocks=True)
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Additionally we need to read and set the self energy::
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Additionally we need to read and set the self energy, the chemical potential and the double counting::
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ar = HDFArchive('case_Sigma.h5', 'a')
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SK.put_Sigma(Sigma_imp = [ar['dmft_transp_output']['Sigma_w']])
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SK.chemical_potential = ar['dmft_transp_output']['chemical_potential']
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SK.dc_imp = ar['dmft_transp_output']['dc_imp']
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del ar
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As next step we can calculate the transport distribution :math:`\Gamma_{\alpha\beta}(\omega)`::
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@ -100,8 +102,8 @@ The parameters are:
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* `directions`: :math:`\alpha` and :math:`\beta` (e.g. xx, yy, xz, ...)
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* `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`.
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The Seebeck coefficient is only calculated if :math:`\Omega=0.0` is included.
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* `energy_window`: Limits for the integration over :math:`\omega`. (Due to the Fermi functions the integrand is only of considerable size in a small
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window around the Fermi energy.)
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* `energy_window`: Limits for the integration over :math:`\omega` (Due to the Fermi functions the integrand is only of considerable size in a small
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window around the Fermi energy). For optical conductivity calculations the window is automatically enlarged by :math:`\Omega` .
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* `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).
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* `broadening`: The numerical broadening should be set to a finite value for with_Sigma = False.
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@ -221,7 +221,7 @@ class Wien2kConverter(ConverterTools):
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"""
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if not (mpi.is_master_node()): return
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mpi.report("Reading parproj input from %s..."%self.parproj_file)
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mpi.report("Reading input from %s..."%self.parproj_file)
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dens_mat_below = [ [numpy.zeros([self.shells[ish]['dim'],self.shells[ish]['dim']],numpy.complex_) for ish in range(self.n_shells)]
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for isp in range(self.n_spin_blocs) ]
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@ -396,7 +396,7 @@ class Wien2kConverter(ConverterTools):
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band_window = [numpy.zeros((n_k, 2), dtype=int) for isp in range(SP + 1 - SO)]
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for isp, f in enumerate(files):
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if not os.path.exists(f): raise IOError, "convert_misc_input: File %s does not exist" %f
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print "Reading input from %s..."%f,
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mpi.report("Reading input from %s..."%f)
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R = ConverterTools.read_fortran_file(self, f, self.fortran_to_replace)
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assert int(R.next()) == n_k, "convert_misc_input: Number of k-points is inconsistent in oubwin file!"
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@ -416,7 +416,7 @@ class Wien2kConverter(ConverterTools):
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# lattice_angles: unit cell angles in rad
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if not (os.path.exists(self.struct_file)) : raise IOError, "convert_misc_input: File %s does not exist" %self.struct_file
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print "Reading input from %s..."%self.struct_file,
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mpi.report("Reading input from %s..."%self.struct_file)
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with open(self.struct_file) as R:
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try:
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@ -434,7 +434,7 @@ class Wien2kConverter(ConverterTools):
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# rot_symmetries: matrix representation of all (space group) symmetry operations
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if not (os.path.exists(self.outputs_file)) : raise IOError, "convert_misc_input: File %s does not exist" %self.outputs_file
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print "Reading input from %s..."%self.outputs_file,
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mpi.report("Reading input from %s..."%self.outputs_file)
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rot_symmetries = []
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with open(self.outputs_file) as R:
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@ -499,7 +499,7 @@ class Wien2kConverter(ConverterTools):
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band_window_optics = []
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for isp, f in enumerate(files):
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if not os.path.exists(f) : raise IOError, "convert_transport_input: File %s does not exist" %f
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print "Reading input from %s..."%f,
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mpi.report("Reading input from %s..."%f)
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R = ConverterTools.read_fortran_file(self, f, {'D':'E','(':'',')':'',',':' '})
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band_window_optics_isp = []
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@ -521,7 +521,7 @@ class Wien2kConverter(ConverterTools):
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if (nu_i != nu_j): velocity_xyz[nu_j][nu_i][i] = velocity_xyz[nu_i][nu_j][i].conjugate()
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velocities_k[isp].append(velocity_xyz)
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band_window_optics.append(numpy.array(band_window_optics_isp))
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print "DONE!"
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R.close() # Reading done!
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# Put data to HDF5 file
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ar = HDFArchive(self.hdf_file, 'a')
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@ -537,7 +537,7 @@ class Wien2kConverter(ConverterTools):
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"""
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if not (mpi.is_master_node()): return
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mpi.report("Reading symmetry input from %s..."%symm_file)
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mpi.report("Reading input from %s..."%symm_file)
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n_orbits = len(orbits)
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@ -480,7 +480,7 @@ class SumkDFTTools(SumkDFT):
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return volumecc, volumepc
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def transport_distribution(self, directions=['xx'], energy_window=None, Om_mesh=[0.0], beta=40, with_Sigma=False, n_om=None, broadening=0.01):
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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):
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"""
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calculate Tr A(k,w) v(k) A(k, w+Om) v(k).
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energy_window: regime for omega integral
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@ -496,13 +496,16 @@ class SumkDFTTools(SumkDFT):
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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
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self.read_transport_input_from_hdf()
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if mpi.is_master_node():
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# k-dependent-projections.
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assert self.k_dep_projection == 1, "transport_distribution: k dependent projection is not implemented!"
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# positive Om_mesh
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assert all(Om >= 0.0 for Om in Om_mesh), "transport_distribution: Om_mesh should not contain negative values!"
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n_inequiv_spin_blocks = self.SP + 1 - self.SO # up and down are equivalent if SP = 0
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self.directions = directions
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dir_to_int = {'x':0, 'y':1, 'z':2}
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dir_to_int = {'x':0, 'y':1, 'z':2}
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# k-dependent-projections.
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assert self.k_dep_projection == 1, "transport_distribution: k dependent projection is not implemented!"
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# calculate A(k,w)
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#######################################
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@ -515,14 +518,14 @@ class SumkDFTTools(SumkDFT):
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print "Using omega mesh provided by Sigma!"
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if energy_window is not None:
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# Find according window in Sigma mesh
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ioffset = numpy.sum(self.omega < energy_window[0])
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self.omega = self.omega[numpy.logical_and(self.omega >= energy_window[0], self.omega <= energy_window[1])]
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# Find according window in Sigma mesh
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ioffset = numpy.sum(self.omega < energy_window[0]-max(Om_mesh))
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self.omega = self.omega[numpy.logical_and(self.omega >= energy_window[0]-max(Om_mesh), self.omega <= energy_window[1]+max(Om_mesh))]
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n_om = len(self.omega)
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# Truncate Sigma to given omega window
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# In the future there should be an option in gf to manipulate the mesh (e.g. truncate) directly.
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# For we stick with this:
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# In the future there should be an option in gf to manipulate the mesh (e.g. truncate) directly.
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# For now we stick with this:
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for icrsh in range(self.n_corr_shells):
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Sigma_save = self.Sigma_imp_w[icrsh].copy()
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spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
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@ -536,10 +539,10 @@ class SumkDFTTools(SumkDFT):
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else:
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assert n_om is not None, "transport_distribution: Number of omega points (n_om) needed to calculate transport distribution!"
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assert energy_window is not None, "transport_distribution: Energy window needed to calculate transport distribution!"
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assert broadening != 0.0 and broadening is not None, "transport_distribution: Broadening necessary to calculate transport distribution!"
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self.omega = numpy.linspace(energy_window[0],energy_window[1],n_om)
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mesh = [energy_window[0], energy_window[1], n_om]
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mu = 0.0
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assert broadening != 0.0 and broadening is not None, "transport_distribution: Broadening necessary to calculate transport distribution!"
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self.omega = numpy.linspace(energy_window[0]-max(Om_mesh),energy_window[1]+max(Om_mesh),n_om)
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mesh = [energy_window[0]-max(Om_mesh), energy_window[1]+max(Om_mesh), n_om]
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mu = 0.0
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# Check if energy_window is sufficiently large
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if (abs(self.fermi_dis(self.omega[0]*beta)*self.fermi_dis(-self.omega[0]*beta)) > 1e-5
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@ -550,7 +553,7 @@ class SumkDFTTools(SumkDFT):
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# Define mesh for optic conductivity
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d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
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iOm_mesh = numpy.array([int(Om / d_omega) for Om in Om_mesh])
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iOm_mesh = numpy.array([round((Om / d_omega),0) for Om in Om_mesh])
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self.Om_mesh = iOm_mesh * d_omega
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if mpi.is_master_node():
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@ -571,7 +574,7 @@ class SumkDFTTools(SumkDFT):
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A_kw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_)
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for isp in range(n_inequiv_spin_blocks)]
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for isp in range(n_inequiv_spin_blocks):
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for isp in range(n_inequiv_spin_blocks):
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# Obtain A_kw from G_w (swapaxes is used to have omega in the 3rd dimension)
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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
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b_min = max(self.band_window[isp][ik, 0], self.band_window_optics[isp][ik, 0])
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@ -588,10 +591,10 @@ class SumkDFTTools(SumkDFT):
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vel_R[nu1][nu2][:] = numpy.dot(R, vel_R[nu1][nu2][:])
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# calculate Gamma_w for each direction from the velocities vel_R and the spectral function A_kw
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for direction in self.directions:
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for direction in self.directions:
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for iw in xrange(n_om):
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for iq in range(len(self.Om_mesh)):
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if(iw + iOm_mesh[iq] >= n_om): continue
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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
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self.Gamma_w[direction][iq, iw] += (numpy.dot(numpy.dot(numpy.dot(vel_R[v_i, v_i, dir_to_int[direction[0]]],
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A_kw[isp][A_i, A_i, iw]), vel_R[v_i, v_i, dir_to_int[direction[1]]]),
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A_kw[isp][A_i, A_i, iw + iOm_mesh[iq]]).trace().real * self.bz_weights[ik])
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@ -649,7 +652,7 @@ class SumkDFTTools(SumkDFT):
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if ~numpy.isnan(A1[direction][iq]):
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# Seebeck is overwritten if there is more than one Omega = 0 in Om_mesh
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self.seebeck[direction] = - A1[direction][iq] / A0[direction][iq] * 86.17
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self.optic_cond[direction] = A0[direction] * 10700.0
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self.optic_cond[direction] = beta * A0[direction] * 10700.0 / numpy.pi
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for iq in xrange(n_q):
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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])
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if not (numpy.isnan(A1[direction][iq])):
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test/SrVO3.h5
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test/SrVO3.h5
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