mirror of
https://github.com/triqs/dft_tools
synced 2024-11-18 12:03:50 +01:00
1450 lines
67 KiB
Python
1450 lines
67 KiB
Python
##########################################################################
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#
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# TRIQS: a Toolbox for Research in Interacting Quantum Systems
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#
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# Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
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#
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# TRIQS is free software: you can redistribute it and/or modify it under the
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# terms of the GNU General Public License as published by the Free Software
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# Foundation, either version 3 of the License, or (at your option) any later
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# version.
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#
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# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
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# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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# details.
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#
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# You should have received a copy of the GNU General Public License along with
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
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##########################################################################
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"""
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Extension to the SumkDFT class with some analyiss tools
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"""
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import sys
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from types import *
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import numpy
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from triqs.gf import *
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import triqs.utility.mpi as mpi
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from .symmetry import *
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from .sumk_dft import SumkDFT
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from scipy.integrate import *
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from scipy.interpolate import *
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if not hasattr(numpy, 'full'):
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# polyfill full for older numpy:
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numpy.full = lambda a, f: numpy.zeros(a) + f
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class SumkDFTTools(SumkDFT):
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"""
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Extends the SumkDFT class with some tools for analysing the data.
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"""
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def __init__(self, hdf_file, h_field=0.0, mesh=None, beta=40, n_iw=1025, use_dft_blocks=False, dft_data='dft_input', symmcorr_data='dft_symmcorr_input',
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parproj_data='dft_parproj_input', symmpar_data='dft_symmpar_input', bands_data='dft_bands_input',
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transp_data='dft_transp_input', misc_data='dft_misc_input'):
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"""
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Initialisation of the class. Parameters are exactly as for SumKDFT.
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"""
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SumkDFT.__init__(self, hdf_file=hdf_file, h_field=h_field, mesh=mesh, beta=beta, n_iw=n_iw,
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use_dft_blocks=use_dft_blocks, dft_data=dft_data, symmcorr_data=symmcorr_data,
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parproj_data=parproj_data, symmpar_data=symmpar_data, bands_data=bands_data,
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transp_data=transp_data, misc_data=misc_data)
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# Uses .data of only GfReFreq objects.
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def dos_wannier_basis(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True):
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"""
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Calculates the density of states in the basis of the Wannier functions.
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Parameters
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----------
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mu : double, optional
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Chemical potential, overrides the one stored in the hdf5 archive.
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broadening : double, optional
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Lorentzian broadening of the spectra. If not given, standard value of lattice_gf is used.
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mesh : real frequency MeshType, optional
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Omega mesh for the real-frequency Green's function. Given as parameter to lattice_gf.
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with_Sigma : boolean, optional
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If True, the self energy is used for the calculation. If false, the DOS is calculated without self energy.
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with_dc : boolean, optional
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If True the double counting correction is used.
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save_to_file : boolean, optional
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If True, text files with the calculated data will be created.
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Returns
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-------
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DOS : Dict of numpy arrays
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Contains the full density of states.
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DOSproj : Dict of numpy arrays
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DOS projected to atoms.
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DOSproj_orb : Dict of numpy arrays
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DOS projected to atoms and resolved into orbital contributions.
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"""
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if mesh is None or with_Sigma:
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assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
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om_mesh = [x.real for x in self.mesh]
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om_min = om_mesh[0]
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om_max = om_mesh[-1]
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n_om = len(om_mesh)
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mesh = (om_min, om_max, n_om)
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else:
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om_min, om_max, n_om = mesh
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om_mesh = numpy.linspace(om_min, om_max, n_om)
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G_loc = []
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for icrsh in range(self.n_corr_shells):
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spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
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glist = [GfReFreq(target_shape=(block_dim, block_dim), window=(om_min, om_max), n_points=n_om)
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for block, block_dim in self.gf_struct_sumk[icrsh]]
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G_loc.append(
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BlockGf(name_list=spn, block_list=glist, make_copies=False))
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for icrsh in range(self.n_corr_shells):
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G_loc[icrsh].zero()
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DOS = {sp: numpy.zeros([n_om], numpy.float_)
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for sp in self.spin_block_names[self.SO]}
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DOSproj = [{} for ish in range(self.n_inequiv_shells)]
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DOSproj_orb = [{} for ish in range(self.n_inequiv_shells)]
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for ish in range(self.n_inequiv_shells):
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for sp in self.spin_block_names[self.corr_shells[self.inequiv_to_corr[ish]]['SO']]:
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dim = self.corr_shells[self.inequiv_to_corr[ish]]['dim']
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DOSproj[ish][sp] = numpy.zeros([n_om], numpy.float_)
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DOSproj_orb[ish][sp] = numpy.zeros(
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[n_om, dim, dim], numpy.complex_)
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ikarray = numpy.array(list(range(self.n_k)))
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for ik in mpi.slice_array(ikarray):
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G_latt_w = self.lattice_gf(
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ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
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G_latt_w *= self.bz_weights[ik]
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# Non-projected DOS
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for iom in range(n_om):
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for bname, gf in G_latt_w:
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DOS[bname][iom] -= gf.data[iom, :, :].imag.trace() / \
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numpy.pi
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# Projected DOS:
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for icrsh in range(self.n_corr_shells):
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tmp = G_loc[icrsh].copy()
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for bname, gf in tmp:
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tmp[bname] << self.downfold(ik, icrsh, bname, G_latt_w[
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bname], gf) # downfolding G
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G_loc[icrsh] += tmp
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# Collect data from mpi:
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for bname in DOS:
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DOS[bname] = mpi.all_reduce(
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mpi.world, DOS[bname], lambda x, y: x + y)
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for icrsh in range(self.n_corr_shells):
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G_loc[icrsh] << mpi.all_reduce(
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mpi.world, G_loc[icrsh], lambda x, y: x + y)
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mpi.barrier()
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# Symmetrize and rotate to local coord. system if needed:
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if self.symm_op != 0:
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G_loc = self.symmcorr.symmetrize(G_loc)
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if self.use_rotations:
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for icrsh in range(self.n_corr_shells):
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for bname, gf in G_loc[icrsh]:
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G_loc[icrsh][bname] << self.rotloc(
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icrsh, gf, direction='toLocal')
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# G_loc can now also be used to look at orbitally-resolved quantities
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for ish in range(self.n_inequiv_shells):
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for bname, gf in G_loc[self.inequiv_to_corr[ish]]: # loop over spins
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DOSproj[ish][bname] = -gf.data.imag.trace(axis1=1, axis2=2) / numpy.pi
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DOSproj_orb[ish][bname][
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:, :, :] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:,:,:]
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# Write to files
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if save_to_file and mpi.is_master_node():
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for sp in self.spin_block_names[self.SO]:
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f = open('DOS_wann_%s.dat' % sp, 'w')
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for iom in range(n_om):
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f.write("%s %s\n" % (om_mesh[iom], DOS[sp][iom]))
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f.close()
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# Partial
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for ish in range(self.n_inequiv_shells):
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f = open('DOS_wann_%s_proj%s.dat' % (sp, ish), 'w')
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for iom in range(n_om):
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f.write("%s %s\n" %
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(om_mesh[iom], DOSproj[ish][sp][iom]))
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f.close()
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# Orbitally-resolved
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for i in range(self.corr_shells[self.inequiv_to_corr[ish]]['dim']):
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for j in range(i, self.corr_shells[self.inequiv_to_corr[ish]]['dim']):
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f = open('DOS_wann_' + sp + '_proj' + str(ish) +
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'_' + str(i) + '_' + str(j) + '.dat', 'w')
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for iom in range(n_om):
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f.write("%s %s %s\n" % (
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om_mesh[iom], DOSproj_orb[ish][sp][iom, i, j].real,DOSproj_orb[ish][sp][iom, i, j].imag))
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f.close()
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return DOS, DOSproj, DOSproj_orb
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def dos_wannier_basis_all(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True):
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"""
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Calculates the density of states in the basis of the Wannier functions.
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Parameters
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----------
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mu : double, optional
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Chemical potential, overrides the one stored in the hdf5 archive.
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broadening : double, optional
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Lorentzian broadening of the spectra. If not given, standard value of lattice_gf is used.
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mesh : real frequency MeshType, optional
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Omega mesh for the real-frequency Green's function. Given as parameter to lattice_gf.
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with_Sigma : boolean, optional
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If True, the self energy is used for the calculation. If false, the DOS is calculated without self energy.
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with_dc : boolean, optional
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If True the double counting correction is used.
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save_to_file : boolean, optional
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If True, text files with the calculated data will be created.
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Returns
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-------
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DOS : Dict of numpy arrays
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Contains the full density of states.
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DOSproj : Dict of numpy arrays
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DOS projected to atoms.
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DOSproj_orb : Dict of numpy arrays
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DOS projected to atoms and resolved into orbital contributions.
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"""
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if mesh is None or with_Sigma:
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assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
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om_mesh = [x.real for x in self.mesh]
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om_min = om_mesh[0]
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om_max = om_mesh[-1]
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n_om = len(om_mesh)
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mesh = (om_min, om_max, n_om)
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else:
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om_min, om_max, n_om = mesh
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om_mesh = numpy.linspace(om_min, om_max, n_om)
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spn = self.spin_block_names[self.SO]
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gf_struct_parproj = [[(sp, list(range(self.shells[ish]['dim']))) for sp in spn]
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for ish in range(self.n_shells)]
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n_local_orbs = self.proj_mat_csc.shape[2]
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gf_struct_parproj_all = [[(sp, list(range(n_local_orbs))) for sp in spn]]
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glist_all = [GfReFreq(target_shape=(block_dim, block_dim), window=(om_min, om_max), n_points=n_om)
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for block, block_dim in gf_struct_parproj_all[0]]
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G_loc_all = BlockGf(name_list=spn, block_list=glist_all, make_copies=False)
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DOS = {sp: numpy.zeros([n_om], numpy.float_)
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for sp in self.spin_block_names[self.SO]}
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DOSproj = {}
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DOSproj_orb = {}
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for sp in self.spin_block_names[self.SO]:
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dim = n_local_orbs
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DOSproj[sp] = numpy.zeros([n_om], numpy.float_)
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DOSproj_orb[sp] = numpy.zeros(
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[n_om, dim, dim], numpy.complex_)
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ikarray = numpy.array(list(range(self.n_k)))
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for ik in mpi.slice_array(ikarray):
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G_latt_w = self.lattice_gf(
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ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
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G_latt_w *= self.bz_weights[ik]
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# Non-projected DOS
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for iom in range(n_om):
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for bname, gf in G_latt_w:
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DOS[bname][iom] -= gf.data[iom, :, :].imag.trace() / \
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numpy.pi
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# Projected DOS:
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for bname, gf in G_latt_w:
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G_loc_all[bname] << self.downfold(ik, 0, bname, gf, G_loc_all[bname], shells='csc')
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# Collect data from mpi:
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for bname in DOS:
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DOS[bname] = mpi.all_reduce(
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mpi.world, DOS[bname], lambda x, y: x + y)
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G_loc_all[bname] << mpi.all_reduce(
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mpi.world, G_loc_all[bname], lambda x, y: x + y)
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mpi.barrier()
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# Symmetrize and rotate to local coord. system if needed:
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#if self.symm_op != 0:
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# G_loc_all = self.symmcorr.symmetrize(G_loc_all)
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# G_loc can now also be used to look at orbitally-resolved quantities
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for bname, gf in G_loc_all: # loop over spins
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DOSproj[bname] = -gf.data.imag.trace(axis1=1, axis2=2) / numpy.pi
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DOSproj_orb[bname][:,:,:] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:,:,:]
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# Write to files
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if save_to_file and mpi.is_master_node():
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for sp in self.spin_block_names[self.SO]:
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f = open('DOS_wann_%s.dat' % sp, 'w')
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for iom in range(n_om):
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f.write("%s %s\n" % (om_mesh[iom], DOS[sp][iom]))
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f.close()
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# Partial
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f = open('DOS_wann_all_%s_proj.dat' % (sp), 'w')
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for iom in range(n_om):
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f.write("%s %s\n" %
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(om_mesh[iom], DOSproj[sp][iom]))
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f.close()
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# Orbitally-resolved
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for i in range(n_local_orbs):
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for j in range(i, n_local_orbs):
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f = open('DOS_wann_all' + sp + '_proj_' + str(i) + '_' + str(j) + '.dat', 'w')
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for iom in range(n_om):
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f.write("%s %s %s\n" % (
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om_mesh[iom], DOSproj_orb[sp][iom, i, j].real,DOSproj_orb[sp][iom, i, j].imag))
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f.close()
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return DOS, DOSproj, DOSproj_orb
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# Uses .data of only GfReFreq objects.
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def dos_parproj_basis(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True):
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"""
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Calculates the orbitally-resolved DOS.
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Different to dos_Wannier_basis is that here we calculate projections also to non-Wannier projectors, in the
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flavour of Wien2k QTL calculatuions.
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Parameters
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----------
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mu : double, optional
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Chemical potential, overrides the one stored in the hdf5 archive.
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broadening : double, optional
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Lorentzian broadening of the spectra. If not given, standard value of lattice_gf is used.
|
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mesh : real frequency MeshType, optional
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Omega mesh for the real-frequency Green's function. Given as parameter to lattice_gf.
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with_Sigma : boolean, optional
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If True, the self energy is used for the calculation. If false, the DOS is calculated without self energy.
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with_dc : boolean, optional
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If True the double counting correction is used.
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save_to_file : boolean, optional
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If True, text files with the calculated data will be created.
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Returns
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-------
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DOS : Dict of numpy arrays
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Contains the full density of states.
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DOSproj : Dict of numpy arrays
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DOS projected to atoms.
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DOSproj_orb : Dict of numpy arrays
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DOS projected to atoms and resolved into orbital contributions.
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"""
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things_to_read = ['n_parproj', 'proj_mat_all',
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'rot_mat_all', 'rot_mat_all_time_inv']
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value_read = self.read_input_from_hdf(
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subgrp=self.parproj_data, things_to_read=things_to_read)
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if not value_read:
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return value_read
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if self.symm_op:
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self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data)
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if mesh is None or with_Sigma:
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assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
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om_mesh = [x.real for x in self.mesh]
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om_min = om_mesh[0]
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om_max = om_mesh[-1]
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n_om = len(om_mesh)
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mesh = (om_min, om_max, n_om)
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else:
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om_min, om_max, n_om = mesh
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om_mesh = numpy.linspace(om_min, om_max, n_om)
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G_loc = []
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spn = self.spin_block_names[self.SO]
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gf_struct_parproj = [[(sp, self.shells[ish]['dim']) for sp in spn]
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for ish in range(self.n_shells)]
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for ish in range(self.n_shells):
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glist = [GfReFreq(target_shape=(block_dim, block_dim), window=(om_min, om_max), n_points=n_om)
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for block, block_dim in gf_struct_parproj[ish]]
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G_loc.append(
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BlockGf(name_list=spn, block_list=glist, make_copies=False))
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for ish in range(self.n_shells):
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G_loc[ish].zero()
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DOS = {sp: numpy.zeros([n_om], numpy.float_)
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for sp in self.spin_block_names[self.SO]}
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DOSproj = [{} for ish in range(self.n_shells)]
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DOSproj_orb = [{} for ish in range(self.n_shells)]
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for ish in range(self.n_shells):
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for sp in self.spin_block_names[self.SO]:
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dim = self.shells[ish]['dim']
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DOSproj[ish][sp] = numpy.zeros([n_om], numpy.float_)
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DOSproj_orb[ish][sp] = numpy.zeros(
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[n_om, dim, dim], numpy.complex_)
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ikarray = numpy.array(list(range(self.n_k)))
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for ik in mpi.slice_array(ikarray):
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G_latt_w = self.lattice_gf(
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ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
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G_latt_w *= self.bz_weights[ik]
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# Non-projected DOS
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for bname, gf in G_latt_w:
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DOS[bname] -= gf.data.imag.trace(axis1=1, axis2=2) / numpy.pi
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# Projected DOS:
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for ish in range(self.n_shells):
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tmp = G_loc[ish].copy()
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for ir in range(self.n_parproj[ish]):
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for bname, gf in tmp:
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tmp[bname] << self.downfold(ik, ish, bname, G_latt_w[
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bname], gf, shells='all', ir=ir)
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G_loc[ish] += tmp
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|
|
|
# Collect data from mpi:
|
|
for bname in DOS:
|
|
DOS[bname] = mpi.all_reduce(
|
|
mpi.world, DOS[bname], lambda x, y: x + y)
|
|
for ish in range(self.n_shells):
|
|
G_loc[ish] << mpi.all_reduce(
|
|
mpi.world, G_loc[ish], lambda x, y: x + y)
|
|
mpi.barrier()
|
|
|
|
# Symmetrize and rotate to local coord. system if needed:
|
|
if self.symm_op != 0:
|
|
G_loc = self.symmpar.symmetrize(G_loc)
|
|
if self.use_rotations:
|
|
for ish in range(self.n_shells):
|
|
for bname, gf in G_loc[ish]:
|
|
G_loc[ish][bname] << self.rotloc(
|
|
ish, gf, direction='toLocal', shells='all')
|
|
|
|
# G_loc can now also be used to look at orbitally-resolved quantities
|
|
for ish in range(self.n_shells):
|
|
for bname, gf in G_loc[ish]:
|
|
DOSproj[ish][bname] = -gf.data.imag.trace(axis1=1, axis2=2) / numpy.pi
|
|
DOSproj_orb[ish][bname][
|
|
:, :, :] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:,:,:]
|
|
|
|
# Write to files
|
|
if save_to_file and mpi.is_master_node():
|
|
for sp in self.spin_block_names[self.SO]:
|
|
f = open('DOS_parproj_%s.dat' % sp, 'w')
|
|
for iom in range(n_om):
|
|
f.write("%s %s\n" % (om_mesh[iom], DOS[sp][iom]))
|
|
f.close()
|
|
|
|
# Partial
|
|
for ish in range(self.n_shells):
|
|
f = open('DOS_parproj_%s_proj%s.dat' % (sp, ish), 'w')
|
|
for iom in range(n_om):
|
|
f.write("%s %s\n" %
|
|
(om_mesh[iom], DOSproj[ish][sp][iom]))
|
|
f.close()
|
|
|
|
# Orbitally-resolved
|
|
for i in range(self.shells[ish]['dim']):
|
|
for j in range(i, self.shells[ish]['dim']):
|
|
f = open('DOS_parproj_' + sp + '_proj' + str(ish) +
|
|
'_' + str(i) + '_' + str(j) + '.dat', 'w')
|
|
for iom in range(n_om):
|
|
f.write("%s %s %s\n" % (
|
|
om_mesh[iom], DOSproj_orb[ish][sp][iom, i, j].real,DOSproj_orb[ish][sp][iom, i, j].imag))
|
|
f.close()
|
|
|
|
return DOS, DOSproj, DOSproj_orb
|
|
|
|
# Elk total and partial dos calculations
|
|
# Uses .data of only GfReFreq objects.
|
|
def elk_dos(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True,pdos=False,nk=None):
|
|
"""
|
|
This calculates the total DOS and the partial DOS (orbital-DOS) from the band characters calculated in Elk.
|
|
|
|
Parameters
|
|
----------
|
|
mu : double, optional
|
|
Chemical potential, overrides the one stored in the hdf5 archive.
|
|
broadening : double, optional
|
|
Lorentzian broadening of the spectra. If not given, standard value of lattice_gf is used.
|
|
mesh : real frequency MeshType, optional
|
|
Omega mesh for the real-frequency Green's function. Given as parameter to lattice_gf.
|
|
with_Sigma : boolean, optional
|
|
If True, the self energy is used for the calculation. If false, the DOS is calculated without self energy.
|
|
with_dc : boolean, optional
|
|
If True the double counting correction is used.
|
|
save_to_file : boolean, optional
|
|
If True, text files with the calculated data will be created.
|
|
pdos : allows the partial density of states to be calculated
|
|
nk : diagonal of the occupation function (from the Matsubara Green's function)
|
|
in the band basis (has form nk[spn][n_k][n_orbital])
|
|
|
|
Returns
|
|
-------
|
|
DOS : Dict of numpy arrays
|
|
Contains the full density of states.
|
|
pDOS : Dict of numpy arrays
|
|
partial (orbital resolved) DOS for each atom.
|
|
"""
|
|
|
|
if (pdos):
|
|
things_to_read = ['maxlm', 'bc']
|
|
value_read = self.read_input_from_hdf(
|
|
subgrp=self.bc_data, things_to_read=things_to_read)
|
|
if not value_read:
|
|
return value_read
|
|
things_to_read = ['n_atoms']
|
|
value_read = self.read_input_from_hdf(
|
|
subgrp=self.symmcorr_data, things_to_read=things_to_read)
|
|
if not value_read:
|
|
return value_read
|
|
|
|
if mesh is None or with_Sigma:
|
|
assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
|
|
om_mesh = [x.real for x in self.mesh]
|
|
om_min = om_mesh[0]
|
|
om_max = om_mesh[-1]
|
|
n_om = len(om_mesh)
|
|
mesh = (om_min, om_max, n_om)
|
|
else:
|
|
om_min, om_max, n_om = mesh
|
|
om_mesh = numpy.linspace(om_min, om_max, n_om)
|
|
if mu is None:
|
|
mu = self.chemical_potential
|
|
|
|
spn = self.spin_block_names[self.SO]
|
|
|
|
DOS = {sp: numpy.zeros([n_om], numpy.float_)
|
|
for sp in self.spin_block_names[self.SO]}
|
|
#set up temporary arrays for pdos calculations
|
|
if (pdos):
|
|
pDOS = {sp: numpy.zeros([self.n_atoms,self.maxlm,n_om], numpy.float_)
|
|
for sp in self.spin_block_names[self.SO]}
|
|
ntoi = self.spin_names_to_ind[self.SO]
|
|
else:
|
|
pDOS = []
|
|
|
|
ikarray = numpy.array(range(self.n_k))
|
|
for ik in mpi.slice_array(ikarray):
|
|
|
|
G_latt_w = self.lattice_gf(
|
|
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
|
|
G_latt_w *= self.bz_weights[ik]
|
|
if(nk!=None):
|
|
for iom in range(n_om):
|
|
for bname, gf in G_latt_w:
|
|
numpy.fill_diagonal(G_latt_w[bname].data[iom,:,:].imag, nk[bname][ik][:]*G_latt_w[bname].data[iom,:,:].imag.diagonal())
|
|
|
|
# Non-projected DOS
|
|
for iom in range(n_om):
|
|
for bname, gf in G_latt_w:
|
|
DOS[bname][iom] -= gf.data[iom, :, :].imag.trace() / \
|
|
numpy.pi
|
|
|
|
|
|
# Partial DOS
|
|
if (pdos):
|
|
for bname, gf in G_latt_w:
|
|
isp=ntoi[bname]
|
|
nst=self.n_orbitals[ik,isp]
|
|
tmp = numpy.zeros([nst])
|
|
for iom in range(n_om):
|
|
#get diagonal spectral function
|
|
tmp[:] = -gf.data[iom, :, :].imag.diagonal() / numpy.pi
|
|
#calculate the pDOS of all atoms
|
|
for iatom in range(self.n_atoms):
|
|
bcar=self.bc[:,isp,iatom,0:nst,ik]
|
|
pDOS[bname][iatom,:,iom] += numpy.matmul(bcar,tmp)
|
|
del tmp
|
|
mpi.barrier()
|
|
# Collect data from mpi:
|
|
for bname in DOS:
|
|
DOS[bname] = mpi.all_reduce(
|
|
mpi.world, DOS[bname], lambda x, y: x + y)
|
|
if (pdos):
|
|
for bname in pDOS:
|
|
for iatom in range(self.n_atoms):
|
|
for lm in range(self.maxlm):
|
|
pDOS[bname][iatom,lm,:] = mpi.all_reduce(
|
|
mpi.world, pDOS[bname][iatom,lm,:], lambda x, y: x + y)
|
|
|
|
|
|
# Write to files
|
|
if save_to_file and mpi.is_master_node():
|
|
for sp in self.spin_block_names[self.SO]:
|
|
f = open('TDOS_%s.dat' % sp, 'w')
|
|
for iom in range(n_om):
|
|
f.write("%s %s\n" % (om_mesh[iom], DOS[sp][iom]))
|
|
f.close()
|
|
|
|
# Partial
|
|
if (pdos):
|
|
for iatom in range(self.n_atoms):
|
|
f = open('pDOS_%s_atom_%s.dat' % (sp, iatom), 'w')
|
|
for lm in range(self.maxlm):
|
|
for iom in range(n_om):
|
|
f.write("%s %s\n" %
|
|
(om_mesh[iom], pDOS[sp][iatom,lm,iom]))
|
|
f.write("\n")
|
|
f.close()
|
|
|
|
return DOS, pDOS
|
|
|
|
# vector manipulation used in Elk for symmetry operations - This is already in elktools, this should
|
|
# put somewhere for general use by the converter and this script.
|
|
def v3frac(self,v,eps):
|
|
#This finds the fractional part of 3-vector v components. This uses the
|
|
#same method as in Elk (version 6.2.8) r3fac subroutine.
|
|
v[0]=v[0]-numpy.floor(v[0])
|
|
if(v[0] < 0): v[0]+=1
|
|
if((1-v[0]) < eps): v[0]=0
|
|
if(v[0] < eps): v[0]=0
|
|
v[1]=v[1]-numpy.floor(v[1])
|
|
if(v[1] < 0): v[1]+=1
|
|
if((1-v[1]) < eps): v[1]=0
|
|
if(v[1] < eps): v[1]=0
|
|
v[2]=v[2]-numpy.floor(v[2])
|
|
if(v[2] < 0): v[2]+=1
|
|
if((1-v[2]) < eps): v[2]=0
|
|
if(v[2] < eps): v[2]=0
|
|
return v
|
|
|
|
# Calculate the spectral function at an energy contour omega - i.e. Fermi surface plots
|
|
# Uses .data of only GfReFreq objects.
|
|
def fs_plot(self, mu=None, broadening=None, mesh=None, FS=True, plane=True, sym=True, orthvec=None, with_Sigma=True, with_dc=True, save_to_file=True):
|
|
"""
|
|
Calculates the correlated spectral function at specific frequencies. The default output is the
|
|
correlated spectral function at zero frequency - this relates the the Fermi surface.
|
|
|
|
Parameters
|
|
----------
|
|
mu : double, optional
|
|
Chemical potential, overrides the one stored in the hdf5 archive.
|
|
broadening : double, optional
|
|
Lorentzian broadening of the spectra. If not given, standard value of lattice_gf is used.
|
|
mesh : real frequency MeshType, optional
|
|
Omega mesh for the real-frequency Green's function. Given as parameter to lattice_gf.
|
|
plane : boolean, optional
|
|
True assumes that the k-mesh of eigenvalues calculated was a plane.
|
|
sym: boolean, optional
|
|
Uses the symmetry operations to fold out the correlated spectral function in the BZ
|
|
FS: boolean
|
|
Flag for calculating the spectral function at the Fermi level (omega->0)
|
|
orthvec: double (3) element numpy array, optional
|
|
This is used to determine the vectors used in the plane calculations after folding out the IBZ.
|
|
This needs to correspond to the same orthonormal LATTICE inputs vectors used in the DFT code
|
|
which generated the plane of energy eigenvalues.
|
|
The default is orthvec=[0,0,1].
|
|
with_Sigma : boolean, optional
|
|
If True, the self energy is used for the calculation. If false, the DOS is calculated without self energy.
|
|
with_dc : boolean, optional
|
|
If True the double counting correction is used.
|
|
save_to_file : boolean, optional
|
|
If True, text files with the calculated data will be created.
|
|
|
|
Returns
|
|
-------
|
|
nk : int
|
|
The number of k-points in the plane.
|
|
vkc : Dict of numpy arrays [shape - (nk, 3)]
|
|
Contains the cartesian vectors which the spectral function has been evaluated on.
|
|
Akw : Dict of numpy arrays [shape - (spn)(self.n_k, n_om)]
|
|
Correlated spectral function - the data as it is written to the files.
|
|
iknr : int array
|
|
An array of k-point indices which mape the Akw over the unfolded BZ.
|
|
"""
|
|
#default vector tolerance used in Elk. This should not be alter.
|
|
epslat=1E-6
|
|
#read in the energy contour energies and projectors
|
|
things_to_read = ['n_k','bmat','symlat','n_symm','vkl',
|
|
'n_orbitals', 'proj_mat', 'hopping']
|
|
value_read = self.read_input_from_hdf(
|
|
subgrp=self.fs_data, things_to_read=things_to_read)
|
|
if not value_read:
|
|
return value_read
|
|
|
|
if with_Sigma is True or mesh is None:
|
|
assert isinstance(self.mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True or mesh is not given"
|
|
om_mesh = [x.real for x in self.mesh]
|
|
#for Fermi Surface calculations
|
|
if FS:
|
|
jw=[i for i in range(len(om_mesh)) if om_mesh[i] == 0.0]
|
|
if len(jw)==0:
|
|
mpi.report('Sigma_imp_w mesh does not include zero frequency value')
|
|
mpi.report('Using the next absolute lowest frequency value.')
|
|
abs_om_mesh = [abs(i) for i in om_mesh]
|
|
jw=[i for i in range(len(abs_om_mesh)) if abs_om_mesh[i] == numpy.min(abs_om_mesh[:])]
|
|
mpi.report(jw)
|
|
#for many energy contour calculations
|
|
else:
|
|
if mesh:
|
|
om_mn=mesh[0]
|
|
om_mx=mesh[1]
|
|
jw=[i for i in range(len(om_mesh)) if((om_mesh[i]<=om_mx)and(om_mesh[i]>=om_mn))]
|
|
om_min = om_mesh[0]
|
|
om_max = om_mesh[-1]
|
|
n_om = len(om_mesh)
|
|
mesh = (om_min, om_max, n_om)
|
|
if broadening is None:
|
|
broadening=0.0
|
|
else:
|
|
#a range of frequencies can be used if desired
|
|
om_min, om_max, n_om = mesh
|
|
om_mesh = numpy.linspace(om_min, om_max, n_om)
|
|
FS=False
|
|
jw=[i for i in range(len(om_mesh)) if((om_mesh[i]<=om_max)and(om_mesh[i]>=om_min))]
|
|
if mu is None:
|
|
mu = self.chemical_potential
|
|
|
|
#orthogonal vector used for plane calculations
|
|
if orthvec is None:
|
|
#set to [0,0,1] by default
|
|
orthvec = numpy.zeros(3,dtype=numpy.float_)
|
|
orthvec[2] = 1.0
|
|
elif orthvec.size != 3:
|
|
assert 0, "The input numpy orthvec is not the required size of 3!"
|
|
|
|
spn = self.spin_block_names[self.SO]
|
|
|
|
Akw = {sp: numpy.zeros([self.n_k, n_om], numpy.float_)
|
|
for sp in spn}
|
|
|
|
#Cartesian lattice coordinates array
|
|
vkc = numpy.zeros([self.n_k,3], numpy.float_)
|
|
|
|
ikarray = numpy.array(range(self.n_k))
|
|
for ik in mpi.slice_array(ikarray):
|
|
#calculate the catesian coordinates of IBZ
|
|
vkc[ik,:] = numpy.matmul(self.bmat,self.vkl[ik,:])
|
|
|
|
G_latt_w = self.lattice_gf(
|
|
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
|
|
|
|
for iom in range(n_om):
|
|
for bname, gf in G_latt_w:
|
|
Akw[bname][ik, iom] += gf.data[iom,:,:].imag.trace() / (-1.0 * numpy.pi)
|
|
mpi.barrier()
|
|
|
|
# Collect data from mpi:
|
|
for sp in spn:
|
|
Akw[sp] = mpi.all_reduce(mpi.world, Akw[sp], lambda x, y: x + y)
|
|
mpi.barrier()
|
|
|
|
#fold out the IBZ k-points using the lattice vectors and symmetries
|
|
#reducible number of k-points (which will alter after out folding)
|
|
nk = self.n_k
|
|
iknr = numpy.arange(self.n_k)
|
|
if sym:
|
|
vkltmp = self.vkl
|
|
v = numpy.zeros(3, numpy.float_)
|
|
v_orth = numpy.zeros(3, numpy.float_)
|
|
for isym in range(self.n_symm):
|
|
#calculate the orthonormal vector after symmetry operation. This is used to
|
|
#check if the orthonormal vector after the symmetry operation is parallel
|
|
#or anit-parallel to the original vector.
|
|
if plane:
|
|
vo = numpy.matmul(self.symlat[isym][:,:],orthvec[:].transpose())
|
|
#check if the vectors are parallel or anti-parallel respectively
|
|
t1 = numpy.array_equal(vo, orthvec)
|
|
if(not t1):
|
|
#exit this symmetry operation
|
|
continue
|
|
|
|
for ik in range(self.n_k):
|
|
#find point in BZ by symmetry operation
|
|
v[:]=numpy.matmul(self.symlat[isym][:,:],self.vkl[ik,:])
|
|
#shift back in to range [0,1) - Elk specific
|
|
v[:]=self.v3frac(v,epslat)
|
|
#add vector to list if not present and add the equivalent Akw value
|
|
#convert to cartesian
|
|
v[:] = numpy.matmul(self.bmat,v[:])
|
|
#alter temporary arrays
|
|
nk += 1
|
|
vkc = numpy.vstack((vkc,v))
|
|
iknr = numpy.append(iknr,ik)
|
|
vkltmp = numpy.vstack((vkltmp,v))
|
|
#remove duplicates
|
|
[vkc,ind]=numpy.unique(vkc,return_index=True,axis=0)
|
|
iknr=iknr[ind]
|
|
nk=vkc.shape[0]
|
|
#sort the indices for output in decending order
|
|
iksrt=numpy.lexsort(([vkc[:,i] for i in range(0,vkc.shape[1], 1)]))
|
|
#rearrange the vkc and iknr arrays
|
|
vkc=vkc[iksrt]
|
|
iknr=iknr[iksrt]
|
|
|
|
# Write to files
|
|
if save_to_file and mpi.is_master_node():
|
|
for sp in self.spin_block_names[self.SO]:
|
|
if FS:
|
|
#Output default FS spectral function
|
|
f = open('Akw_FS_%s.dat' % sp, 'w')
|
|
for ik in range(nk):
|
|
jk=iknr[ik]
|
|
f.write("%s %s %s %s\n" % (vkc[ik,0], vkc[ik,1], vkc[ik,2], Akw[bname][jk, jw[0]]))
|
|
f.close()
|
|
else:
|
|
#Output spectral function from multiple frequencies
|
|
for iom in jw:
|
|
#output the energy contours in multiple files with mesh index.
|
|
f = open('Akw_%s_omega_%s.dat' % (sp, iom), 'w')
|
|
for ik in range(nk):
|
|
jk=iknr[ik]
|
|
f.write("%s %s %s %s %s\n" % (vkc[ik,0], vkc[ik,1], vkc[ik,2], om_mesh[iom], Akw[bname][jk, iom]))
|
|
f.close()
|
|
return nk, vkc, Akw, iknr
|
|
|
|
|
|
|
|
# Uses .data of only GfReFreq objects.
|
|
def spaghettis(self, broadening=None, plot_shift=0.0, plot_range=None, ishell=None, mu=None, save_to_file='Akw_'):
|
|
"""
|
|
Calculates the correlated band structure using a real-frequency self energy.
|
|
|
|
Parameters
|
|
----------
|
|
mu : double, optional
|
|
Chemical potential, overrides the one stored in the hdf5 archive.
|
|
broadening : double, optional
|
|
Lorentzian broadening of the spectra. If not given, standard value of lattice_gf is used.
|
|
plot_shift : double, optional
|
|
Offset for each A(k,w) for stacked plotting of spectra.
|
|
plot_range : list of double, optional
|
|
Sets the energy window for plotting to (plot_range[0],plot_range[1]). If not provided, the energy mesh of the self energy is used.
|
|
ishell : integer, optional
|
|
Contains the index of the shell on which the spectral function is projected. If ishell=None, the total spectrum without projection is calculated.
|
|
save_to_file : string, optional
|
|
Filename where the spectra are stored.
|
|
|
|
Returns
|
|
-------
|
|
Akw : Dict of numpy arrays
|
|
Data as it is also written to the files.
|
|
"""
|
|
|
|
# check if ReFreqMesh is given
|
|
assert isinstance(self.mesh, MeshReFreq)
|
|
|
|
things_to_read = ['n_k', 'n_orbitals', 'proj_mat',
|
|
'hopping', 'n_parproj', 'proj_mat_all']
|
|
value_read = self.read_input_from_hdf(
|
|
subgrp=self.bands_data, things_to_read=things_to_read)
|
|
if not value_read:
|
|
return value_read
|
|
if ishell:
|
|
things_to_read = ['rot_mat_all', 'rot_mat_all_time_inv']
|
|
value_read = self.read_input_from_hdf(
|
|
subgrp=self.parproj_data, things_to_read=things_to_read)
|
|
if not value_read:
|
|
return value_read
|
|
|
|
if mu is None:
|
|
mu = self.chemical_potential
|
|
spn = self.spin_block_names[self.SO]
|
|
mesh = numpy.array([x.value for x in self.mesh])
|
|
n_om = len(mesh)
|
|
|
|
if plot_range is None:
|
|
om_minplot = mesh[0] - 0.001
|
|
om_maxplot = mesh[-1] + 0.001
|
|
else:
|
|
om_minplot = plot_range[0]
|
|
om_maxplot = plot_range[1]
|
|
n_om = len(mesh[(mesh > om_minplot)&(mesh < om_maxplot)])
|
|
|
|
if ishell is None:
|
|
Akw = {sp: numpy.zeros([self.n_k, n_om], numpy.float_)
|
|
for sp in spn}
|
|
else:
|
|
Akw = {sp: numpy.zeros(
|
|
[self.shells[ishell]['dim'], self.n_k, n_om], numpy.float_) for sp in spn}
|
|
|
|
if ishell is not None:
|
|
gf_struct_parproj = [
|
|
(sp, self.shells[ishell]['dim']) for sp in spn]
|
|
G_loc = BlockGf(name_block_generator=[(block, GfReFreq(target_shape=(block_dim, block_dim), mesh=self.Sigma_imp[0].mesh))
|
|
for block, block_dim in gf_struct_parproj], make_copies=False)
|
|
G_loc.zero()
|
|
|
|
ikarray = numpy.array(list(range(self.n_k)))
|
|
for ik in mpi.slice_array(ikarray):
|
|
|
|
G_latt_w = self.lattice_gf(ik=ik, mu=mu, broadening=broadening)
|
|
|
|
if ishell is None:
|
|
# Non-projected A(k,w)
|
|
for bname, gf in G_latt_w:
|
|
Akw[bname][ik] = -gf.data[numpy.where((mesh > om_minplot)&(mesh < om_maxplot))].imag.trace(axis1=1, axis2=2)/numpy.pi
|
|
# shift Akw for plotting stacked k-resolved eps(k)
|
|
# curves
|
|
Akw[bname][ik] += ik * plot_shift
|
|
|
|
else: # ishell not None
|
|
# Projected A(k,w):
|
|
G_loc.zero()
|
|
tmp = G_loc.copy()
|
|
for ir in range(self.n_parproj[ishell]):
|
|
for bname, gf in tmp:
|
|
tmp[bname] << self.downfold(ik, ishell, bname, G_latt_w[
|
|
bname], gf, shells='all', ir=ir)
|
|
G_loc += tmp
|
|
|
|
# Rotate to local frame
|
|
if self.use_rotations:
|
|
for bname, gf in G_loc:
|
|
G_loc[bname] << self.rotloc(
|
|
ishell, gf, direction='toLocal', shells='all')
|
|
|
|
for ish in range(self.shells[ishell]['dim']):
|
|
for sp in spn:
|
|
Akw[sp][ish, ik] = -gf.data[numpy.where((mesh > om_minplot)&(mesh < om_maxplot))].imag.trace(axis1=1, axis2=2)/numpy.pi
|
|
# Collect data from mpi
|
|
for sp in spn:
|
|
Akw[sp] = mpi.all_reduce(mpi.world, Akw[sp], lambda x, y: x + y)
|
|
mpi.barrier()
|
|
|
|
if save_to_file and mpi.is_master_node():
|
|
if ishell is None:
|
|
for sp in spn: # loop over GF blocs:
|
|
# Open file for storage:
|
|
f = open(save_to_file + sp + '.dat', 'w')
|
|
for ik in range(self.n_k):
|
|
for iom in range(n_om):
|
|
if (mesh[iom] > om_minplot) and (mesh[iom] < om_maxplot):
|
|
if plot_shift > 0.0001:
|
|
f.write('%s %s\n' %
|
|
(mesh[iom], Akw[sp][ik, iom]))
|
|
else:
|
|
f.write('%s %s %s\n' %
|
|
(ik, mesh[iom], Akw[sp][ik, iom]))
|
|
f.write('\n')
|
|
f.close()
|
|
|
|
else: # ishell is not None
|
|
for sp in spn:
|
|
for ish in range(self.shells[ishell]['dim']):
|
|
# Open file for storage:
|
|
f = open(save_to_file + str(ishell) + '_' +
|
|
sp + '_proj' + str(ish) + '.dat', 'w')
|
|
for ik in range(self.n_k):
|
|
for iom in range(n_om):
|
|
if (mesh[iom] > om_minplot) and (mesh[iom] < om_maxplot):
|
|
if plot_shift > 0.0001:
|
|
f.write('%s %s\n' % (
|
|
mesh[iom], Akw[sp][ish, ik, iom]))
|
|
else:
|
|
f.write('%s %s %s\n' % (
|
|
ik, mesh[iom], Akw[sp][ish, ik, iom]))
|
|
f.write('\n')
|
|
f.close()
|
|
|
|
return Akw
|
|
|
|
def partial_charges(self, mu=None, with_Sigma=True, with_dc=True):
|
|
"""
|
|
Calculates the orbitally-resolved density matrix for all the orbitals considered in the input, consistent with
|
|
the definition of Wien2k. Hence, (possibly non-orthonormal) projectors have to be provided in the partial projectors subgroup of
|
|
the hdf5 archive.
|
|
|
|
Parameters
|
|
----------
|
|
|
|
with_Sigma : boolean, optional
|
|
If True, the self energy is used for the calculation. If false, partial charges are calculated without self-energy correction.
|
|
mu : double, optional
|
|
Chemical potential, overrides the one stored in the hdf5 archive.
|
|
with_dc : boolean, optional
|
|
If True the double counting correction is used.
|
|
|
|
Returns
|
|
-------
|
|
dens_mat : list of numpy array
|
|
A list of density matrices projected to all shells provided in the input.
|
|
"""
|
|
|
|
things_to_read = ['dens_mat_below', 'n_parproj',
|
|
'proj_mat_all', 'rot_mat_all', 'rot_mat_all_time_inv']
|
|
value_read = self.read_input_from_hdf(
|
|
subgrp=self.parproj_data, things_to_read=things_to_read)
|
|
if not value_read:
|
|
return value_read
|
|
if self.symm_op:
|
|
self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data)
|
|
|
|
spn = self.spin_block_names[self.SO]
|
|
ntoi = self.spin_names_to_ind[self.SO]
|
|
# Density matrix in the window
|
|
self.dens_mat_window = [[numpy.zeros([self.shells[ish]['dim'], self.shells[ish]['dim']], numpy.complex_)
|
|
for ish in range(self.n_shells)]
|
|
for isp in range(len(spn))]
|
|
# Set up G_loc
|
|
gf_struct_parproj = [[(sp, self.shells[ish]['dim']) for sp in spn]
|
|
for ish in range(self.n_shells)]
|
|
G_loc = [BlockGf(name_block_generator=[(block, GfImFreq(target_shape=(block_dim, block_dim), mesh=self.mesh))
|
|
for block, block_dim in gf_struct_parproj[ish]], make_copies=False)
|
|
for ish in range(self.n_shells)]
|
|
for ish in range(self.n_shells):
|
|
G_loc[ish].zero()
|
|
|
|
ikarray = numpy.array(list(range(self.n_k)))
|
|
for ik in mpi.slice_array(ikarray):
|
|
|
|
G_latt_iw = self.lattice_gf(ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc)
|
|
G_latt_iw *= self.bz_weights[ik]
|
|
for ish in range(self.n_shells):
|
|
tmp = G_loc[ish].copy()
|
|
for ir in range(self.n_parproj[ish]):
|
|
for bname, gf in tmp:
|
|
tmp[bname] << self.downfold(ik, ish, bname, G_latt_iw[
|
|
bname], gf, shells='all', ir=ir)
|
|
G_loc[ish] += tmp
|
|
|
|
# Collect data from mpi:
|
|
for ish in range(self.n_shells):
|
|
G_loc[ish] << mpi.all_reduce(
|
|
mpi.world, G_loc[ish], lambda x, y: x + y)
|
|
mpi.barrier()
|
|
|
|
# Symmetrize and rotate to local coord. system if needed:
|
|
if self.symm_op != 0:
|
|
G_loc = self.symmpar.symmetrize(G_loc)
|
|
if self.use_rotations:
|
|
for ish in range(self.n_shells):
|
|
for bname, gf in G_loc[ish]:
|
|
G_loc[ish][bname] << self.rotloc(
|
|
ish, gf, direction='toLocal', shells='all')
|
|
|
|
for ish in range(self.n_shells):
|
|
isp = 0
|
|
for bname, gf in G_loc[ish]:
|
|
self.dens_mat_window[isp][ish] = G_loc[ish].density()[bname]
|
|
isp += 1
|
|
|
|
# Add density matrices to get the total:
|
|
dens_mat = [[self.dens_mat_below[ntoi[spn[isp]]][ish] + self.dens_mat_window[isp][ish]
|
|
for ish in range(self.n_shells)]
|
|
for isp in range(len(spn))]
|
|
|
|
return dens_mat
|
|
|
|
def print_hamiltonian(self):
|
|
"""
|
|
Prints the Kohn-Sham Hamiltonian to the text files hamup.dat and hamdn.dat (no spin orbit-coupling), or to ham.dat (with spin-orbit coupling).
|
|
"""
|
|
|
|
if self.SP == 1 and self.SO == 0:
|
|
f1 = open('hamup.dat', 'w')
|
|
f2 = open('hamdn.dat', 'w')
|
|
for ik in range(self.n_k):
|
|
for i in range(self.n_orbitals[ik, 0]):
|
|
f1.write('%s %s\n' %
|
|
(ik, self.hopping[ik, 0, i, i].real))
|
|
for i in range(self.n_orbitals[ik, 1]):
|
|
f2.write('%s %s\n' %
|
|
(ik, self.hopping[ik, 1, i, i].real))
|
|
f1.write('\n')
|
|
f2.write('\n')
|
|
f1.close()
|
|
f2.close()
|
|
else:
|
|
f = open('ham.dat', 'w')
|
|
for ik in range(self.n_k):
|
|
for i in range(self.n_orbitals[ik, 0]):
|
|
f.write('%s %s\n' %
|
|
(ik, self.hopping[ik, 0, i, i].real))
|
|
f.write('\n')
|
|
f.close()
|
|
|
|
|
|
# ----------------- transport -----------------------
|
|
|
|
def read_transport_input_from_hdf(self):
|
|
r"""
|
|
Reads the data for transport calculations from the hdf5 archive.
|
|
"""
|
|
thingstoread = ['band_window_optics', 'velocities_k']
|
|
self.read_input_from_hdf(
|
|
subgrp=self.transp_data, things_to_read=thingstoread)
|
|
thingstoread = ['band_window', 'lattice_angles', 'lattice_constants',
|
|
'lattice_type', 'n_symmetries', 'rot_symmetries']
|
|
self.read_input_from_hdf(
|
|
subgrp=self.misc_data, things_to_read=thingstoread)
|
|
|
|
def cellvolume(self, lattice_type, lattice_constants, latticeangle):
|
|
r"""
|
|
Determines the conventional und primitive unit cell volumes.
|
|
|
|
Parameters
|
|
----------
|
|
lattice_type : string
|
|
Lattice type according to the Wien2k convention (P, F, B, R, H, CXY, CYZ, CXZ).
|
|
lattice_constants : list of double
|
|
Lattice constants (a, b, c).
|
|
lattice angles : list of double
|
|
Lattice angles (:math:`\alpha, \beta, \gamma`).
|
|
|
|
Returns
|
|
-------
|
|
vol_c : double
|
|
Conventional unit cell volume.
|
|
vol_p : double
|
|
Primitive unit cell volume.
|
|
"""
|
|
|
|
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])
|
|
vol_c = a * b * c * \
|
|
numpy.sqrt(1 + 2 * c_al * c_be * c_ga -
|
|
c_al ** 2 - c_be ** 2 - c_ga ** 2)
|
|
|
|
det = {"P": 1, "F": 4, "B": 2, "R": 3,
|
|
"H": 1, "CXY": 2, "CYZ": 2, "CXZ": 2}
|
|
vol_p = vol_c / det[lattice_type]
|
|
|
|
return vol_c, vol_p
|
|
|
|
# Uses .data of only GfReFreq objects.
|
|
def transport_distribution(self, beta, directions=['xx'], energy_window=None, Om_mesh=[0.0], with_Sigma=False, n_om=None, broadening=0.0):
|
|
r"""
|
|
Calculates the transport distribution
|
|
|
|
.. math::
|
|
\Gamma_{\alpha\beta}\left(\omega+\Omega/2, \omega-\Omega/2\right) = \frac{1}{V} \sum_k Tr\left(v_{k,\alpha}A_{k}(\omega+\Omega/2)v_{k,\beta}A_{k}\left(\omega-\Omega/2\right)\right)
|
|
|
|
in the direction :math:`\alpha\beta`. The velocities :math:`v_{k}` are read from the transport subgroup of the hdf5 archive.
|
|
|
|
Parameters
|
|
----------
|
|
|
|
beta : double
|
|
Inverse temperature :math:`\beta`.
|
|
directions : list of double, optional
|
|
:math:`\alpha\beta` e.g.: ['xx','yy','zz','xy','xz','yz'].
|
|
energy_window : list of double, optional
|
|
Specifies the upper and lower limit of the frequency integration for :math:`\Omega=0.0`. The window is automatically enlarged by the largest :math:`\Omega` value,
|
|
hence the integration is performed in the interval [energy_window[0]-max(Om_mesh), energy_window[1]+max(Om_mesh)].
|
|
Om_mesh : list of double, optional
|
|
:math:`\Omega` frequency mesh of the optical conductivity. For the conductivity and the Seebeck coefficient :math:`\Omega=0.0` has to be
|
|
part of the mesh. In the current version Om_mesh is repined to the mesh provided by the self-energy! The actual mesh is printed on the screen and stored as
|
|
member Om_mesh.
|
|
with_Sigma : boolean, optional
|
|
Determines whether the calculation is performed with or without self energy. If this parameter is set to False the self energy is set to zero (i.e. the DFT band
|
|
structure :math:`A(k,\omega)` is used). Note: For with_Sigma=False it is necessary to specify the parameters energy_window, n_om and broadening.
|
|
n_om : integer, optional
|
|
Number of equidistant frequency points in the interval [energy_window[0]-max(Om_mesh), energy_window[1]+max(Om_mesh)]. This parameters is only used if
|
|
with_Sigma = False.
|
|
broadening : double, optional
|
|
Lorentzian broadening. It is necessary to specify the boradening if with_Sigma = False, otherwise this parameter can be set to 0.0.
|
|
"""
|
|
|
|
# Check if wien converter was called and read transport subgroup form
|
|
# hdf file
|
|
if mpi.is_master_node():
|
|
ar = HDFArchive(self.hdf_file, 'r')
|
|
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)
|
|
# check if outputs file was converted
|
|
if not ('n_symmetries' in ar['dft_misc_input']):
|
|
raise IOError("transport_distribution: n_symmetries missing. Check if case.outputs file is present and call convert_misc_input() or convert_dft_input().")
|
|
|
|
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!"
|
|
|
|
# Check if energy_window is sufficiently large and correct
|
|
|
|
if (energy_window[0] >= energy_window[1] or energy_window[0] >= 0 or energy_window[1] <= 0):
|
|
assert 0, "transport_distribution: energy_window wrong!"
|
|
|
|
if (abs(self.fermi_dis(energy_window[0], beta) * self.fermi_dis(-energy_window[0], beta)) > 1e-5
|
|
or abs(self.fermi_dis(energy_window[1], beta) * self.fermi_dis(-energy_window[1], beta)) > 1e-5):
|
|
mpi.report(
|
|
"\n####################################################################")
|
|
mpi.report(
|
|
"transport_distribution: WARNING - energy window might be too narrow!")
|
|
mpi.report(
|
|
"####################################################################\n")
|
|
|
|
# up and down are equivalent if SP = 0
|
|
n_inequiv_spin_blocks = self.SP + 1 - self.SO
|
|
self.directions = directions
|
|
dir_to_int = {'x': 0, 'y': 1, 'z': 2}
|
|
|
|
# calculate A(k,w)
|
|
#######################################
|
|
|
|
# Define mesh for Green's function and in the specified energy window
|
|
if (with_Sigma == True):
|
|
self.omega = numpy.array([round(x.real, 12)
|
|
for x in self.mesh])
|
|
mesh = None
|
|
mu = self.chemical_potential
|
|
n_om = len(self.omega)
|
|
mpi.report("Using omega mesh provided by Sigma!")
|
|
|
|
if energy_window:
|
|
# 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 now we stick with this:
|
|
for icrsh in range(self.n_corr_shells):
|
|
Sigma_save = self.Sigma_imp[icrsh].copy()
|
|
spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
|
|
glist = lambda: [GfReFreq(target_shape=(block_dim, block_dim), window=(self.omega[
|
|
0], self.omega[-1]), n_points=n_om) for block, block_dim in self.gf_struct_sumk[icrsh]]
|
|
self.Sigma_imp[icrsh] = BlockGf(
|
|
name_list=spn, block_list=glist(), make_copies=False)
|
|
for i, g in self.Sigma_imp[icrsh]:
|
|
for iL in g.indices[0]:
|
|
for iR in g.indices[0]:
|
|
for iom in range(n_om):
|
|
g.data[iom, int(iL), int(iR)] = Sigma_save[
|
|
i].data[ioffset + iom, int(iL), int(iR)]
|
|
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] - 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
|
|
|
|
# Define mesh for optic conductivity
|
|
d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
|
|
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():
|
|
print("Chemical potential: ", mu)
|
|
print("Using n_om = %s points in the energy_window [%s,%s]" % (n_om, self.omega[0], self.omega[-1]), end=' ')
|
|
print("where the omega vector is:")
|
|
print(self.omega)
|
|
print("Calculation requested for Omega mesh: ", numpy.array(Om_mesh))
|
|
print("Omega mesh automatically repined to: ", self.Om_mesh)
|
|
|
|
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(list(range(self.n_k)))
|
|
for ik in mpi.slice_array(ikarray):
|
|
# Calculate G_w for ik and initialize A_kw
|
|
G_w = self.lattice_gf(ik, mu, 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)]
|
|
|
|
for isp in range(n_inequiv_spin_blocks):
|
|
# copy data from G_w (swapaxes is used to have omega in the 3rd
|
|
# dimension)
|
|
A_kw[isp] = copy.deepcopy(G_w[self.spin_block_names[self.SO][
|
|
isp]].data.swapaxes(0, 1).swapaxes(1, 2))
|
|
# calculate A(k,w) for each frequency
|
|
for iw in range(n_om):
|
|
A_kw[isp][:, :, iw] = -1.0 / (2.0 * numpy.pi * 1j) * (
|
|
A_kw[isp][:, :, iw] - numpy.conjugate(numpy.transpose(A_kw[isp][:, :, iw])))
|
|
|
|
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)
|
|
|
|
# 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 range(n_om):
|
|
for iq in range(len(self.Om_mesh)):
|
|
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, int(iw + iOm_mesh[iq])]), vel_R[v_i, v_i, dir_to_int[direction[1]]]),
|
|
A_kw[isp][A_i, A_i, iw]).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 transport_coefficient(self, direction, iq, n, beta, method=None):
|
|
r"""
|
|
Calculates the transport coefficient A_n in a given direction for a given :math:`\Omega`. The required members (Gamma_w, directions, Om_mesh) have to be obtained first
|
|
by calling the function :meth:`transport_distribution <dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`. For n>0 A is set to NaN if :math:`\Omega` is not 0.0.
|
|
|
|
Parameters
|
|
----------
|
|
direction : string
|
|
:math:`\alpha\beta` e.g.: 'xx','yy','zz','xy','xz','yz'.
|
|
iq : integer
|
|
Index of :math:`\Omega` point in the member Om_mesh.
|
|
n : integer
|
|
Number of the desired moment of the transport distribution.
|
|
beta : double
|
|
Inverse temperature :math:`\beta`.
|
|
method : string
|
|
Integration method: cubic spline and scipy.integrate.quad ('quad'), simpson rule ('simps'), trapezoidal rule ('trapz'), rectangular integration (otherwise)
|
|
Note that the sampling points of the the self-energy are used!
|
|
|
|
Returns
|
|
-------
|
|
A : double
|
|
Transport coefficient.
|
|
"""
|
|
|
|
if not (mpi.is_master_node()):
|
|
return
|
|
|
|
assert hasattr(
|
|
self, 'Gamma_w'), "transport_coefficient: Run transport_distribution first or load data from h5!"
|
|
|
|
if (self.Om_mesh[iq] == 0.0 or n == 0.0):
|
|
A = 0.0
|
|
# setup the integrand
|
|
if (self.Om_mesh[iq] == 0.0):
|
|
A_int = self.Gamma_w[direction][iq] * (self.fermi_dis(
|
|
self.omega, beta) * self.fermi_dis(-self.omega, beta)) * (self.omega * beta)**n
|
|
elif (n == 0.0):
|
|
A_int = self.Gamma_w[direction][iq] * (self.fermi_dis(self.omega, beta) - self.fermi_dis(
|
|
self.omega + self.Om_mesh[iq], beta)) / (self.Om_mesh[iq] * beta)
|
|
|
|
# w-integration
|
|
if method == 'quad':
|
|
# quad on interpolated w-points with cubic spline
|
|
A_int_interp = interp1d(self.omega, A_int, kind='cubic')
|
|
A = quad(A_int_interp, min(self.omega), max(self.omega),
|
|
epsabs=1.0e-12, epsrel=1.0e-12, limit=500)
|
|
A = A[0]
|
|
elif method == 'simps':
|
|
# simpson rule for w-grid
|
|
A = simps(A_int, self.omega)
|
|
elif method == 'trapz':
|
|
# trapezoidal rule for w-grid
|
|
A = numpy.trapz(A_int, self.omega)
|
|
else:
|
|
# rectangular integration for w-grid (orignal implementation)
|
|
d_w = self.omega[1] - self.omega[0]
|
|
for iw in range(self.Gamma_w[direction].shape[1]):
|
|
A += A_int[iw] * d_w
|
|
A = A * numpy.pi * (2.0 - self.SP)
|
|
else:
|
|
A = numpy.nan
|
|
return A
|
|
|
|
def conductivity_and_seebeck(self, beta, method=None):
|
|
r"""
|
|
Calculates the Seebeck coefficient and the optical conductivity by calling
|
|
:meth:`transport_coefficient <dft.sumk_dft_tools.SumkDFTTools.transport_coefficient>`.
|
|
The required members (Gamma_w, directions, Om_mesh) have to be obtained first by calling the function
|
|
:meth:`transport_distribution <dft.sumk_dft_tools.SumkDFTTools.transport_distribution>`.
|
|
|
|
Parameters
|
|
----------
|
|
beta : double
|
|
Inverse temperature :math:`\beta`.
|
|
|
|
Returns
|
|
-------
|
|
optic_cond : dictionary of double vectors
|
|
Optical conductivity in each direction and frequency given by Om_mesh.
|
|
|
|
seebeck : dictionary of double
|
|
Seebeck coefficient in each direction. If zero is not present in Om_mesh the Seebeck coefficient is set to NaN.
|
|
|
|
kappa : dictionary of double.
|
|
thermal conductivity in each direction. If zero is not present in Om_mesh the thermal conductivity is set to NaN
|
|
"""
|
|
|
|
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}
|
|
A2 = {direction: numpy.full((n_q,), numpy.nan)
|
|
for direction in self.directions}
|
|
self.seebeck = {direction: numpy.nan for direction in self.directions}
|
|
self.kappa = {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 range(n_q):
|
|
A0[direction][iq] = self.transport_coefficient(
|
|
direction, iq=iq, n=0, beta=beta, method=method)
|
|
A1[direction][iq] = self.transport_coefficient(
|
|
direction, iq=iq, n=1, beta=beta, method=method)
|
|
A2[direction][iq] = self.transport_coefficient(
|
|
direction, iq=iq, n=2, beta=beta, method=method)
|
|
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]))
|
|
print("A_2 in direction %s for Omega = %.2f %e a.u." % (direction, self.Om_mesh[iq], A2[direction][iq]))
|
|
if ~numpy.isnan(A1[direction][iq]):
|
|
# Seebeck and kappa are overwritten if there is more than one Omega =
|
|
# 0 in Om_mesh
|
|
self.seebeck[direction] = - \
|
|
A1[direction][iq] / A0[direction][iq] * 86.17
|
|
self.kappa[direction] = A2[direction][iq] - A1[direction][iq]*A1[direction][iq]/A0[direction][iq]
|
|
self.kappa[direction] *= 293178.0
|
|
self.optic_cond[direction] = beta * \
|
|
A0[direction] * 10700.0 / numpy.pi
|
|
for iq in range(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]))
|
|
print("kappa in direction %s for Omega = 0.00 %f W/(m * K)" % (direction, self.kappa[direction]))
|
|
|
|
return self.optic_cond, self.seebeck, self.kappa
|
|
|
|
|
|
def fermi_dis(self, w, beta):
|
|
r"""
|
|
Fermi distribution.
|
|
|
|
.. math::
|
|
f(x) = 1/(e^x+1).
|
|
|
|
Parameters
|
|
----------
|
|
w : double
|
|
frequency
|
|
beta : double
|
|
inverse temperature
|
|
|
|
Returns
|
|
-------
|
|
f : double
|
|
"""
|
|
return 1.0 / (numpy.exp(w * beta) + 1)
|