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Code Issues Releases Wiki Activity

[transport] API changes

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This commit is contained in:
Manuel Zingl 2014-11-20 13:17:46 +01:00 committed by Priyanka Seth
parent 9283702fc1
commit e1b8c4757b
3 changed files with 294 additions and 10 deletions
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17
python/converters/wien2k_converter.py
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@ -24,6 +24,7 @@ from types import *
import numpy, os.path
from pytriqs.archive import *
from converter_tools import *
import os.path
class Wien2kConverter(ConverterTools):
"""
@ -61,7 +62,7 @@ class Wien2kConverter(ConverterTools):
# Checks if h5 file is there and repacks it if wanted:
if (os.path.exists(self.hdf_file) and repacking):
ConverterTools.repack(self)
def convert_dft_input(self):
"""
@ -378,10 +379,10 @@ class Wien2kConverter(ConverterTools):
# Check if SP, SO and n_k are already in h5
ar = HDFArchive(self.hdf_file, 'a')
if not (self.lda_subgrp in ar): raise IOError, "No SumK_LDA subgroup in hdf file found! Call convert_dmft_input first."
SP = ar[self.lda_subgrp]['SP']
SO = ar[self.lda_subgrp]['SO']
n_k = ar[self.lda_subgrp]['n_k']
if not (self.dft_subgrp in ar): raise IOError, "No %s subgroup in hdf file found! Call convert_dmft_input first." %self.dft_subgrp
SP = ar[self.dft_subgrp]['SP']
SO = ar[self.dft_subgrp]['SO']
n_k = ar[self.dft_subgrp]['n_k']
del ar
# Read relevant data from .pmat file
@ -512,15 +513,15 @@ class Wien2kConverter(ConverterTools):
if(SP == 0 or SO == 1):
if not (os.path.exists(self.oubwin_file)) : raise IOError, "File %s does not exist" %self.oubwin_file
print "Reading input from %s..."%self.oubwin_file
f = read_fortran_file(self.oubwin_file)
f = ConverterTools.read_fortran_file(self, self.oubwin_file, self.fortran_to_replace)
elif (SP == 1 and isp == 0):
if not (os.path.exists(self.oubwin_file+'up')) : raise IOError, "File %s does not exist" %self.oubwin_file+'up'
print "Reading input from %s..."%self.oubwin_file+'up'
f = read_fortran_file(self.oubwin_file+'up')
f = ConverterTools.read_fortran_file(self, self.oubwin_file+'up', self.fortran_to_replace)
elif (SP == 1 and isp ==1):
if not (os.path.exists(self.oubwin_file+'dn')) : raise IOError, "File %s does not exist" %self.oubwin_file+'dn'
print "Reading input from %s..."%self.oubwin_file+'dn'
f = read_fortran_file(self.oubwin_file+'dn')
f = ConverterTools.read_fortran_file(self, self.oubwin_file+'dn', self.fortran_to_replace)
else:
assert 0, "Reding oubwin error! Check SP and SO!"
assert int(f.next()) == n_k, "Number of k-points is unconsistent in oubwin file!"

4
python/sumk_dft.py
View File

@ -34,7 +34,7 @@ class SumkDFT:
def __init__(self, hdf_file, h_field = 0.0, use_dft_blocks = False,
dft_data = 'dft_input', symmcorr_data = 'dft_symmcorr_input', parproj_data = 'dft_parproj_input',
symmpar_data = 'dft_symmpar_input', bands_data = 'dft_bands_input'):
symmpar_data = 'dft_symmpar_input', bands_data = 'dft_bands_input', transp_data = 'dft_transp_input'):
"""
Initialises the class from data previously stored into an HDF5
"""
@ -48,6 +48,7 @@ class SumkDFT:
self.parproj_data = parproj_data
self.symmpar_data = symmpar_data
self.bands_data = bands_data
self.transp_data = transp_data
self.G_upfold = None
self.h_field = h_field
@ -97,6 +98,7 @@ class SumkDFT:
# Analyse the block structure and determine the smallest gf_struct blocks and maps, if desired
if use_dft_blocks: self.analyse_block_structure()
################
# HDF5 FUNCTIONS
################

283
python/sumk_dft_tools.py
View File

@ -38,7 +38,7 @@ class SumkDFTTools(SumkDFT):
self.G_upfold_refreq = None
SumkDFT.__init__(self, hdf_file=hdf_file, h_field=h_field, use_dft_blocks=use_dft_blocks,
dft_data=dft_data, symmcorr_data=symmcorr_data, parproj_data=parproj_data,
symmpar_data=symmpar_data, bands_data=bands_data)
symmpar_data=symmpar_data, bands_data=bands_data, transp_data=transp_data)
def downfold_pc(self,ik,ir,ish,bname,gf_to_downfold,gf_inp):
@ -557,3 +557,284 @@ class SumkDFTTools(SumkDFT):
for isp in range(len(spn)) ]
return dens_mat
def read_transport_input_from_hdf(self):
"""
Reads the data for transport calculations from the HDF file
"""
thingstoread = ['bandwin','bandwin_opt','kp','latticeangles','latticeconstants','latticetype','nsymm','symmcartesian','vk']
retval = self.read_input_from_hdf(subgrp=self.transp_data,things_to_read = thingstoread)
return retval
def cellvolume(self, latticetype, latticeconstants, latticeangle):
"""
Calculate cell volume: volumecc conventional cell, volumepc, primitive cell.
"""
a = latticeconstants[0]
b = latticeconstants[1]
c = latticeconstants[2]
c_al = numpy.cos(latticeangle[0])
c_be = numpy.cos(latticeangle[1])
c_ga = numpy.cos(latticeangle[2])
volumecc = a * b * c * numpy.sqrt(1 + 2 * c_al * c_be * c_ga - c_al ** 2 - c_be * 82 - c_ga ** 2)
det = {"P":1, "F":4, "B":2, "R":3, "H":1, "CXY":2, "CYZ":2, "CXZ":2}
volumepc = volumecc / det[latticetype]
return volumecc, volumepc
def fermidis(self, x):
return 1.0/(numpy.exp(x)+1)
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'):
"""calculate Tr A(k,w) v(k) A(k, w+q) v(k) and optics.
energywindow: regime for omega integral
Om_mesh: contains the frequencies of the optic conductivitity. Om_mesh is repinned to the self-energy mesh
(hence exact values might be different from those given in Om_mesh)
dir_list: list to defines the indices of directions. xx,yy,zz,xy,yz,zx.
((0, 0) --> xx, (1, 1) --> yy, (0, 2) --> xz, default: (0, 0))
DFT_only: Use Sigma = 0 (Issue to solve: code still needs self-energy for mesh)
"""
# Check if wien converter was called
if mpi.is_master_node():
ar = HDFArchive(self.hdf_file, 'a')
if not (self.transp_data in ar): raise IOError, "No %s subgroup in hdf file found! Call convert_transp_input first." %self.transp_data
self.dir_list = dir_list
self.read_transport_input_from_hdf()
velocities = self.vk
self.n_spin_blocks_input = self.SP + 1 - self.SO
# calculate A(k,w)
#######################################
# use k-dependent-projections.
assert self.k_dep_projection == 1, "Not implemented!"
# Define mesh for Greens function and the used energy range
if (DFT_only == False):
self.omega = numpy.array([round(x.real,12) for x in self.Sigma_imp[0].mesh])
mu = self.chemical_potential
n_om = len(self.omega)
print "Using omega mesh provided by Sigma."
if energywindow is not None:
# Find according window in Sigma mesh
ioffset = numpy.sum(self.omega < energywindow[0])
self.omega = self.omega[numpy.logical_and(self.omega >= energywindow[0], self.omega <= energywindow[1])]
n_om = len(self.omega)
# Truncate Sigma to given omega window
for icrsh in range(self.n_corr_shells):
Sigma_save = self.Sigma_imp[icrsh].copy()
spn = self.spin_block_names[self.corr_shells[icrsh][4]]
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]]
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:
for iR in g.indices:
for iom in xrange(n_om):
g.data[iom,iL,iR]= Sigma_save[i].data[ioffset+iom,iL,iR]
else:
assert n_om is not None, "Number of omega points (n_om) needed!"
assert energywindow is not None, "Energy window needed!"
self.omega = numpy.linspace(energywindow[0],energywindow[1],n_om)
mu = 0.0
if (abs(self.fermidis(self.omega[0]*beta)*self.fermidis(-self.omega[0]*beta)) > 1e-5
or abs(self.fermidis(self.omega[-1]*beta)*self.fermidis(-self.omega[-1]*beta)) > 1e-5):
print "\n##########################################"
print "WARNING: Energywindow might be too narrow!"
print "##########################################\n"
d_omega = round(numpy.abs(self.omega[0] - self.omega[1]), 12)
# define exact mesh for optic conductivity
Om_mesh_ex = numpy.array([int(x / d_omega) for x in Om_mesh])
self.Om_meshr= Om_mesh_ex*d_omega
if mpi.is_master_node():
print "Chemical potential: ", mu
print "Using n_om = %s points in the energywindow [%s,%s]"%(n_om, self.omega[0], self.omega[-1])
print "omega vector is:"
print self.omega
print "Omega mesh interval ", d_omega
print "Provided Om_mesh ", numpy.array(Om_mesh)
print "Pinnend Om_mesh to ", self.Om_meshr
# output P(\omega)_xy should have the same dimension as defined in mshape.
self.Pw_optic = numpy.zeros((len(dir_list), len(Om_mesh_ex), n_om), dtype=numpy.float_)
ik = 0
bln = self.spin_block_names[self.SO]
ntoi = self.spin_names_to_ind[self.SO]
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))
for isp in range(self.n_spin_blocks_input) ], make_copies=False)
mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(self.n_spin_blocks_input)] # construct mupat
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)]
ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray):
unchangesize = all([ self.n_orbitals[ik][isp] == mupat[isp].shape[0] for isp in range(self.n_spin_blocks_input)])
if (not unchangesize):
# recontruct green functions.
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))
for isp in range(self.n_spin_blocks_input) ], make_copies=False)
# construct mupat
mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(self.n_spin_blocks_input)]
#set a temporary array storing spectral functions with band index. Note, usually we should have spin index
Annkw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_) for isp in range(self.n_spin_blocks_input)]
# get lattice green function
S <<= 1*Omega + 1j*broadening
MS = copy.deepcopy(mupat)
for ibl in range(self.n_spin_blocks_input):
ind = ntoi[bln[ibl]]
n_orb = self.n_orbitals[ik][ibl]
MS[ibl] = self.hopping[ik,ind,0:n_orb,0:n_orb].real - mupat[ibl]
S -= MS
if (DFT_only == False):
tmp = S.copy() # init temporary storage
# form self energy from impurity self energy and double counting term.
stmp = self.add_dc()
## substract self energy
for icrsh in xrange(self.n_corr_shells):
for sig, gf in tmp: tmp[sig] <<= self.upfold(ik, icrsh, sig, stmp[icrsh][sig], gf)
S -= tmp
S.invert()
for isp in range(self.n_spin_blocks_input):
Annkw[isp].real = -copy.deepcopy(S[self.spin_block_names[self.SO][isp]].data.swapaxes(0,1).swapaxes(1,2)).imag / numpy.pi
for isp in range(self.n_spin_blocks_input):
if(ik%100==0):
print "ik,isp", ik, isp
kvel = velocities[isp][ik]
Pwtem = numpy.zeros((len(dir_list), len(Om_mesh_ex), n_om), dtype=numpy.float_)
bmin = max(self.bandwin[isp][ik, 0], self.bandwin_opt[isp][ik, 0])
bmax = min(self.bandwin[isp][ik, 1], self.bandwin_opt[isp][ik, 1])
Astart = bmin - self.bandwin[isp][ik, 0]
Aend = bmax - self.bandwin[isp][ik, 0] + 1
vstart = bmin - self.bandwin_opt[isp][ik, 0]
vend = bmax - self.bandwin_opt[isp][ik, 0] + 1
#symmetry loop
for Rmat in self.symmcartesian:
# get new velocity.
Rkvel = copy.deepcopy(kvel)
for vnb1 in xrange(self.bandwin_opt[isp][ik, 1] - self.bandwin_opt[isp][ik, 0] + 1):
for vnb2 in xrange(self.bandwin_opt[isp][ik, 1] - self.bandwin_opt[isp][ik, 0] + 1):
Rkvel[vnb1][vnb2][:] = numpy.dot(Rmat, Rkvel[vnb1][vnb2][:])
ipw = 0
for (ir, ic) in dir_list:
for iw in xrange(n_om):
for iq in range(len(Om_mesh_ex)):
if(iw + Om_mesh_ex[iq] >= n_om):
continue
# construct matrix for A and velocity.
Annkwl = Annkw[isp][Astart:Aend, Astart:Aend, iw]
Annkwr = Annkw[isp][Astart:Aend, Astart:Aend, iw + Om_mesh_ex[iq]]
Rkveltr = Rkvel[vstart:vend, vstart:vend, ir]
Rkveltc = Rkvel[vstart:vend, vstart:vend, ic]
# print Annkwl.shape, Annkwr.shape, Rkveltr.shape, Rkveltc.shape
Pwtem[ipw, iq, iw] += numpy.dot(numpy.dot(numpy.dot(Rkveltr, Annkwl), Rkveltc), Annkwr).trace().real
ipw += 1
# k sum and spin sum.
self.Pw_optic += Pwtem * self.bz_weights[ik] / self.nsymm
self.Pw_optic = mpi.all_reduce(mpi.world, self.Pw_optic, lambda x, y : x + y)
self.Pw_optic *= (2 - self.SP)
# put data to h5
# If res_sugrp exists data will be overwritten!
if mpi.is_master_node():
if not (res_subgrp in ar): ar.create_group(res_subgrp)
things_to_save = ['Pw_optic', 'Om_meshr', 'omega', 'dir_list']
for it in things_to_save: ar[res_subgrp][it] = getattr(self, it)
del ar
def conductivity_and_seebeck(self, beta=40, read_hdf=True, res_subgrp='transp_output'):
""" #return 1/T*A0, that is Conductivity in unit 1/V
calculate, save and return Conductivity
"""
if mpi.is_master_node():
if read_hdf:
things_to_read1 = ['Pw_optic','Om_meshr','omega','dir_list']
things_to_read2 = ['latticetype', 'latticeconstants', 'latticeangles']
read_value1 = self.read_input_from_hdf(subgrp = res_subgrp, things_to_read = things_to_read1)
read_value2 = self.read_input_from_hdf(subgrp = self.transp_data, things_to_read = things_to_read2)
if not read_value1 and read_value2: return read_value
else:
assert not hasattr(self,'Pw_optic'), "Run transport_distribution first or set read_hdf = True"
volcc, volpc = self.cellvolume(self.latticetype, self.latticeconstants, self.latticeangles)
L1,L2,L3= self.Pw_optic.shape
omegaT = self.omega * beta
A0 = numpy.empty((L1,L2), dtype=numpy.float_)
q_0 = False
Seebeck = numpy.zeros((L1, 1), dtype=numpy.float_)
Seebeck[:] = numpy.NAN
d_omega = self.omega[1] - self.omega[0]
for iq in xrange(L2):
# treat q = 0, caclulate conductivity and seebeck
if (self.Om_meshr[iq] == 0.0):
# if Om_meshr contains multiple entries with w=0, A1 is overwritten!
q_0 = True
A1 = numpy.zeros((L1, 1), dtype=numpy.float_)
for im in xrange(L1):
for iw in xrange(L3):
A0[im, iq] += beta * self.Pw_optic[im, iq, iw] * self.fermidis(omegaT[iw]) * self.fermidis(-omegaT[iw])
A1[im] += beta * self.Pw_optic[im, iq, iw] * self.fermidis(omegaT[iw]) * self.fermidis(-omegaT[iw]) * numpy.float(omegaT[iw])
Seebeck[im] = -A1[im] / A0[im, iq]
print "A0", A0[im, iq] *d_omega/beta
print "A1", A1[im, iq] *d_omega/beta
# 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