mirror of https://github.com/triqs/dft_tools
[transport] API changes
This commit is contained in:
Manuel Zingl
Priyanka Seth
parent
9283702fc1
commit
e1b8c4757b
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@ -24,6 +24,7 @@ from types import *
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import numpy, os.path
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from pytriqs.archive import *
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from converter_tools import *
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import os.path
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class Wien2kConverter(ConverterTools):
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"""
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@ -61,7 +62,7 @@ class Wien2kConverter(ConverterTools):
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# Checks if h5 file is there and repacks it if wanted:
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if (os.path.exists(self.hdf_file) and repacking):
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ConverterTools.repack(self)
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def convert_dft_input(self):
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"""
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@ -378,10 +379,10 @@ class Wien2kConverter(ConverterTools):
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# Check if SP, SO and n_k are already in h5
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ar = HDFArchive(self.hdf_file, 'a')
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if not (self.lda_subgrp in ar): raise IOError, "No SumK_LDA subgroup in hdf file found! Call convert_dmft_input first."
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SP = ar[self.lda_subgrp]['SP']
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SO = ar[self.lda_subgrp]['SO']
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n_k = ar[self.lda_subgrp]['n_k']
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if not (self.dft_subgrp in ar): raise IOError, "No %s subgroup in hdf file found! Call convert_dmft_input first." %self.dft_subgrp
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SP = ar[self.dft_subgrp]['SP']
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SO = ar[self.dft_subgrp]['SO']
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n_k = ar[self.dft_subgrp]['n_k']
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del ar
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# Read relevant data from .pmat file
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@ -512,15 +513,15 @@ class Wien2kConverter(ConverterTools):
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if(SP == 0 or SO == 1):
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if not (os.path.exists(self.oubwin_file)) : raise IOError, "File %s does not exist" %self.oubwin_file
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print "Reading input from %s..."%self.oubwin_file
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f = read_fortran_file(self.oubwin_file)
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f = ConverterTools.read_fortran_file(self, self.oubwin_file, self.fortran_to_replace)
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elif (SP == 1 and isp == 0):
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if not (os.path.exists(self.oubwin_file+'up')) : raise IOError, "File %s does not exist" %self.oubwin_file+'up'
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print "Reading input from %s..."%self.oubwin_file+'up'
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f = read_fortran_file(self.oubwin_file+'up')
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f = ConverterTools.read_fortran_file(self, self.oubwin_file+'up', self.fortran_to_replace)
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elif (SP == 1 and isp ==1):
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if not (os.path.exists(self.oubwin_file+'dn')) : raise IOError, "File %s does not exist" %self.oubwin_file+'dn'
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print "Reading input from %s..."%self.oubwin_file+'dn'
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f = read_fortran_file(self.oubwin_file+'dn')
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f = ConverterTools.read_fortran_file(self, self.oubwin_file+'dn', self.fortran_to_replace)
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else:
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assert 0, "Reding oubwin error! Check SP and SO!"
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assert int(f.next()) == n_k, "Number of k-points is unconsistent in oubwin file!"
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@ -34,7 +34,7 @@ class SumkDFT:
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def __init__(self, hdf_file, h_field = 0.0, use_dft_blocks = False,
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dft_data = 'dft_input', symmcorr_data = 'dft_symmcorr_input', parproj_data = 'dft_parproj_input',
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symmpar_data = 'dft_symmpar_input', bands_data = 'dft_bands_input'):
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symmpar_data = 'dft_symmpar_input', bands_data = 'dft_bands_input', transp_data = 'dft_transp_input'):
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"""
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Initialises the class from data previously stored into an HDF5
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"""
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@ -48,6 +48,7 @@ class SumkDFT:
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self.parproj_data = parproj_data
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self.symmpar_data = symmpar_data
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self.bands_data = bands_data
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self.transp_data = transp_data
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self.G_upfold = None
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self.h_field = h_field
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@ -97,6 +98,7 @@ class SumkDFT:
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# Analyse the block structure and determine the smallest gf_struct blocks and maps, if desired
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if use_dft_blocks: self.analyse_block_structure()
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################
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# HDF5 FUNCTIONS
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################
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@ -38,7 +38,7 @@ class SumkDFTTools(SumkDFT):
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self.G_upfold_refreq = None
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SumkDFT.__init__(self, hdf_file=hdf_file, h_field=h_field, use_dft_blocks=use_dft_blocks,
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dft_data=dft_data, symmcorr_data=symmcorr_data, parproj_data=parproj_data,
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symmpar_data=symmpar_data, bands_data=bands_data)
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symmpar_data=symmpar_data, bands_data=bands_data, transp_data=transp_data)
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def downfold_pc(self,ik,ir,ish,bname,gf_to_downfold,gf_inp):
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@ -557,3 +557,284 @@ class SumkDFTTools(SumkDFT):
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for isp in range(len(spn)) ]
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return dens_mat
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def read_transport_input_from_hdf(self):
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"""
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Reads the data for transport calculations from the HDF file
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"""
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thingstoread = ['bandwin','bandwin_opt','kp','latticeangles','latticeconstants','latticetype','nsymm','symmcartesian','vk']
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retval = self.read_input_from_hdf(subgrp=self.transp_data,things_to_read = thingstoread)
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return retval
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def cellvolume(self, latticetype, latticeconstants, latticeangle):
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"""
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Calculate cell volume: volumecc conventional cell, volumepc, primitive cell.
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"""
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a = latticeconstants[0]
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b = latticeconstants[1]
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c = latticeconstants[2]
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c_al = numpy.cos(latticeangle[0])
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c_be = numpy.cos(latticeangle[1])
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c_ga = numpy.cos(latticeangle[2])
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volumecc = a * b * c * numpy.sqrt(1 + 2 * c_al * c_be * c_ga - c_al ** 2 - c_be * 82 - c_ga ** 2)
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det = {"P":1, "F":4, "B":2, "R":3, "H":1, "CXY":2, "CYZ":2, "CXZ":2}
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volumepc = volumecc / det[latticetype]
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return volumecc, volumepc
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def fermidis(self, x):
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return 1.0/(numpy.exp(x)+1)
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def transport_distribution(self, dir_list=[(0,0)], broadening=0.01, energywindow=None, Om_mesh=[0.0], beta=40, DFT_only=False, n_om=None, res_subgrp='transp_output'):
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"""calculate Tr A(k,w) v(k) A(k, w+q) v(k) and optics.
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energywindow: regime for omega integral
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Om_mesh: contains the frequencies of the optic conductivitity. Om_mesh is repinned to the self-energy mesh
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(hence exact values might be different from those given in Om_mesh)
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dir_list: list to defines the indices of directions. xx,yy,zz,xy,yz,zx.
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((0, 0) --> xx, (1, 1) --> yy, (0, 2) --> xz, default: (0, 0))
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DFT_only: Use Sigma = 0 (Issue to solve: code still needs self-energy for mesh)
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"""
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# Check if wien converter was called
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if mpi.is_master_node():
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ar = HDFArchive(self.hdf_file, 'a')
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if not (self.transp_data in ar): raise IOError, "No %s subgroup in hdf file found! Call convert_transp_input first." %self.transp_data
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self.dir_list = dir_list
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self.read_transport_input_from_hdf()
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velocities = self.vk
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self.n_spin_blocks_input = self.SP + 1 - self.SO
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# calculate A(k,w)
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#######################################
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# use k-dependent-projections.
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assert self.k_dep_projection == 1, "Not implemented!"
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# Define mesh for Greens function and the used energy range
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if (DFT_only == False):
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self.omega = numpy.array([round(x.real,12) for x in self.Sigma_imp[0].mesh])
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mu = self.chemical_potential
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n_om = len(self.omega)
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print "Using omega mesh provided by Sigma."
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if energywindow is not None:
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# Find according window in Sigma mesh
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ioffset = numpy.sum(self.omega < energywindow[0])
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self.omega = self.omega[numpy.logical_and(self.omega >= energywindow[0], self.omega <= energywindow[1])]
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n_om = len(self.omega)
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# Truncate Sigma to given omega window
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for icrsh in range(self.n_corr_shells):
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Sigma_save = self.Sigma_imp[icrsh].copy()
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spn = self.spin_block_names[self.corr_shells[icrsh][4]]
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glist = lambda : [ GfReFreq(indices = inner, window=(self.omega[0], self.omega[-1]),n_points=n_om) for block, inner in self.gf_struct_sumk[icrsh]]
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self.Sigma_imp[icrsh] = BlockGf(name_list = spn, block_list = glist(),make_copies=False)
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for i,g in self.Sigma_imp[icrsh]:
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for iL in g.indices:
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for iR in g.indices:
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for iom in xrange(n_om):
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g.data[iom,iL,iR]= Sigma_save[i].data[ioffset+iom,iL,iR]
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else:
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assert n_om is not None, "Number of omega points (n_om) needed!"
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assert energywindow is not None, "Energy window needed!"
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self.omega = numpy.linspace(energywindow[0],energywindow[1],n_om)
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mu = 0.0
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if (abs(self.fermidis(self.omega[0]*beta)*self.fermidis(-self.omega[0]*beta)) > 1e-5
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or abs(self.fermidis(self.omega[-1]*beta)*self.fermidis(-self.omega[-1]*beta)) > 1e-5):
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print "\n##########################################"
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print "WARNING: Energywindow might be too narrow!"
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print "##########################################\n"
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d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
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# define exact mesh for optic conductivity
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Om_mesh_ex = numpy.array([int(x / d_omega) for x in Om_mesh])
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self.Om_meshr= Om_mesh_ex*d_omega
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if mpi.is_master_node():
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print "Chemical potential: ", mu
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print "Using n_om = %s points in the energywindow [%s,%s]"%(n_om, self.omega[0], self.omega[-1])
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print "omega vector is:"
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print self.omega
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print "Omega mesh interval ", d_omega
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print "Provided Om_mesh ", numpy.array(Om_mesh)
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print "Pinnend Om_mesh to ", self.Om_meshr
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# output P(\omega)_xy should have the same dimension as defined in mshape.
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self.Pw_optic = numpy.zeros((len(dir_list), len(Om_mesh_ex), n_om), dtype=numpy.float_)
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ik = 0
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bln = self.spin_block_names[self.SO]
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ntoi = self.spin_names_to_ind[self.SO]
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S = BlockGf(name_block_generator=[(bln[isp], GfReFreq(indices=range(self.n_orbitals[ik][isp]), window=(self.omega[0], self.omega[-1]), n_points = n_om))
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for isp in range(self.n_spin_blocks_input) ], make_copies=False)
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mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(self.n_spin_blocks_input)] # construct mupat
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Annkw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_) for isp in range(self.n_spin_blocks_input)]
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ikarray = numpy.array(range(self.n_k))
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for ik in mpi.slice_array(ikarray):
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unchangesize = all([ self.n_orbitals[ik][isp] == mupat[isp].shape[0] for isp in range(self.n_spin_blocks_input)])
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if (not unchangesize):
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# recontruct green functions.
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S = BlockGf(name_block_generator=[(bln[isp], GfReFreq(indices=range(self.n_orbitals[ik][isp]), window = (self.omega[0], self.omega[-1]), n_points = n_om))
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for isp in range(self.n_spin_blocks_input) ], make_copies=False)
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# construct mupat
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mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(self.n_spin_blocks_input)]
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#set a temporary array storing spectral functions with band index. Note, usually we should have spin index
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Annkw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_) for isp in range(self.n_spin_blocks_input)]
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# get lattice green function
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S <<= 1*Omega + 1j*broadening
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MS = copy.deepcopy(mupat)
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for ibl in range(self.n_spin_blocks_input):
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ind = ntoi[bln[ibl]]
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n_orb = self.n_orbitals[ik][ibl]
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MS[ibl] = self.hopping[ik,ind,0:n_orb,0:n_orb].real - mupat[ibl]
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S -= MS
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if (DFT_only == False):
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tmp = S.copy() # init temporary storage
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# form self energy from impurity self energy and double counting term.
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stmp = self.add_dc()
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## substract self energy
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for icrsh in xrange(self.n_corr_shells):
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for sig, gf in tmp: tmp[sig] <<= self.upfold(ik, icrsh, sig, stmp[icrsh][sig], gf)
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S -= tmp
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S.invert()
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for isp in range(self.n_spin_blocks_input):
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Annkw[isp].real = -copy.deepcopy(S[self.spin_block_names[self.SO][isp]].data.swapaxes(0,1).swapaxes(1,2)).imag / numpy.pi
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for isp in range(self.n_spin_blocks_input):
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if(ik%100==0):
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print "ik,isp", ik, isp
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kvel = velocities[isp][ik]
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Pwtem = numpy.zeros((len(dir_list), len(Om_mesh_ex), n_om), dtype=numpy.float_)
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bmin = max(self.bandwin[isp][ik, 0], self.bandwin_opt[isp][ik, 0])
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bmax = min(self.bandwin[isp][ik, 1], self.bandwin_opt[isp][ik, 1])
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Astart = bmin - self.bandwin[isp][ik, 0]
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Aend = bmax - self.bandwin[isp][ik, 0] + 1
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vstart = bmin - self.bandwin_opt[isp][ik, 0]
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vend = bmax - self.bandwin_opt[isp][ik, 0] + 1
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#symmetry loop
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for Rmat in self.symmcartesian:
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# get new velocity.
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Rkvel = copy.deepcopy(kvel)
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for vnb1 in xrange(self.bandwin_opt[isp][ik, 1] - self.bandwin_opt[isp][ik, 0] + 1):
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for vnb2 in xrange(self.bandwin_opt[isp][ik, 1] - self.bandwin_opt[isp][ik, 0] + 1):
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Rkvel[vnb1][vnb2][:] = numpy.dot(Rmat, Rkvel[vnb1][vnb2][:])
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ipw = 0
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for (ir, ic) in dir_list:
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for iw in xrange(n_om):
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for iq in range(len(Om_mesh_ex)):
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if(iw + Om_mesh_ex[iq] >= n_om):
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continue
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# construct matrix for A and velocity.
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Annkwl = Annkw[isp][Astart:Aend, Astart:Aend, iw]
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Annkwr = Annkw[isp][Astart:Aend, Astart:Aend, iw + Om_mesh_ex[iq]]
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Rkveltr = Rkvel[vstart:vend, vstart:vend, ir]
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Rkveltc = Rkvel[vstart:vend, vstart:vend, ic]
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# print Annkwl.shape, Annkwr.shape, Rkveltr.shape, Rkveltc.shape
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Pwtem[ipw, iq, iw] += numpy.dot(numpy.dot(numpy.dot(Rkveltr, Annkwl), Rkveltc), Annkwr).trace().real
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ipw += 1
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# k sum and spin sum.
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self.Pw_optic += Pwtem * self.bz_weights[ik] / self.nsymm
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self.Pw_optic = mpi.all_reduce(mpi.world, self.Pw_optic, lambda x, y : x + y)
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self.Pw_optic *= (2 - self.SP)
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# put data to h5
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# If res_sugrp exists data will be overwritten!
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if mpi.is_master_node():
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if not (res_subgrp in ar): ar.create_group(res_subgrp)
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things_to_save = ['Pw_optic', 'Om_meshr', 'omega', 'dir_list']
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for it in things_to_save: ar[res_subgrp][it] = getattr(self, it)
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del ar
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def conductivity_and_seebeck(self, beta=40, read_hdf=True, res_subgrp='transp_output'):
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""" #return 1/T*A0, that is Conductivity in unit 1/V
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calculate, save and return Conductivity
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"""
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if mpi.is_master_node():
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if read_hdf:
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things_to_read1 = ['Pw_optic','Om_meshr','omega','dir_list']
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things_to_read2 = ['latticetype', 'latticeconstants', 'latticeangles']
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read_value1 = self.read_input_from_hdf(subgrp = res_subgrp, things_to_read = things_to_read1)
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read_value2 = self.read_input_from_hdf(subgrp = self.transp_data, things_to_read = things_to_read2)
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if not read_value1 and read_value2: return read_value
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else:
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assert not hasattr(self,'Pw_optic'), "Run transport_distribution first or set read_hdf = True"
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volcc, volpc = self.cellvolume(self.latticetype, self.latticeconstants, self.latticeangles)
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L1,L2,L3= self.Pw_optic.shape
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omegaT = self.omega * beta
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A0 = numpy.empty((L1,L2), dtype=numpy.float_)
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q_0 = False
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Seebeck = numpy.zeros((L1, 1), dtype=numpy.float_)
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Seebeck[:] = numpy.NAN
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d_omega = self.omega[1] - self.omega[0]
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for iq in xrange(L2):
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# treat q = 0, caclulate conductivity and seebeck
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if (self.Om_meshr[iq] == 0.0):
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# if Om_meshr contains multiple entries with w=0, A1 is overwritten!
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q_0 = True
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A1 = numpy.zeros((L1, 1), dtype=numpy.float_)
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for im in xrange(L1):
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for iw in xrange(L3):
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A0[im, iq] += beta * self.Pw_optic[im, iq, iw] * self.fermidis(omegaT[iw]) * self.fermidis(-omegaT[iw])
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A1[im] += beta * self.Pw_optic[im, iq, iw] * self.fermidis(omegaT[iw]) * self.fermidis(-omegaT[iw]) * numpy.float(omegaT[iw])
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Seebeck[im] = -A1[im] / A0[im, iq]
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print "A0", A0[im, iq] *d_omega/beta
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print "A1", A1[im, iq] *d_omega/beta
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# treat q ~= 0, calculate optical conductivity
|
||||
else:
|
||||
for im in xrange(L1):
|
||||
for iw in xrange(L3):
|
||||
A0[im, iq] += self.Pw_optic[im, iq, iw] * (self.fermidis(omegaT[iw]) - self.fermidis(omegaT[iw] + self.Om_meshr[iq] * beta)) / self.Om_meshr[iq]
|
||||
|
||||
A0 *= d_omega
|
||||
#cond = beta * self.tdintegral(beta, 0)[index]
|
||||
print "V in bohr^3 ", volpc
|
||||
# transform to standard unit as in resistivity
|
||||
OpticCon = A0 * 10700.0 / volpc
|
||||
Seebeck *= 86.17
|
||||
|
||||
# print
|
||||
for im in xrange(L1):
|
||||
for iq in xrange(L2):
|
||||
print "Conductivity in direction %s for Om_mesh %d %.4f x 10^4 Ohm^-1 cm^-1" % (self.dir_list[im], iq, OpticCon[im, iq])
|
||||
print "Resistivity in dircection %s for Om_mesh %d %.4f x 10^-4 Ohm cm" % (self.dir_list[im], iq, 1.0 / OpticCon[im, iq])
|
||||
if q_0:
|
||||
print "Seebeck in direction %s for q = 0 %.4f x 10^(-6) V/K" % (self.dir_list[im], Seebeck[im])
|
||||
|
||||
|
||||
ar = HDFArchive(self.hdf_file, 'a')
|
||||
if not (res_subgrp in ar): ar.create_group(res_subgrp)
|
||||
things_to_save = ['Seebeck', 'OpticCon']
|
||||
for it in things_to_save: ar[res_subgrp][it] = locals()[it]
|
||||
ar[res_subgrp]['Seebeck'] = Seebeck
|
||||
ar[res_subgrp]['OpticCon'] = OpticCon
|
||||
del ar
|
||||
|
||||
return OpticCon, Seebeck
|
||||
|
|
|
|||
Loading…
Reference in New Issue