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[transport] Tidying up, API

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Priyanka Seth 2014-12-09 18:24:50 +01:00
parent 6fb8d9c5cd
commit cc3a9deaa8
3 changed files with 49 additions and 46 deletions
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python/sumk_dft_tools.py
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@ -559,6 +559,7 @@ class SumkDFTTools(SumkDFT):
return dens_mat return dens_mat
# ----------------- transport -----------------------
def read_transport_input_from_hdf(self): def read_transport_input_from_hdf(self):
""" """
@ -588,17 +589,14 @@ class SumkDFTTools(SumkDFT):
return volumecc, volumepc return volumecc, volumepc
def fermidis(self, x): def transport_distribution(self, dir_list=[(0,0)], broadening=0.01, energywindow=None, Om_mesh=[0.0], beta=40, with_Sigma=False, n_om=None, save_hdf=True, res_subgrp='transp_output'):
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, save_hdf=True, res_subgrp='transp_output'):
"""calculate Tr A(k,w) v(k) A(k, w+q) v(k) and optics. """calculate Tr A(k,w) v(k) A(k, w+q) v(k) and optics.
energywindow: regime for omega integral energywindow: regime for omega integral
Om_mesh: contains the frequencies of the optic conductivitity. Om_mesh is repinned to the self-energy mesh 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) (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. 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)) ((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) with_Sigma: Use Sigma = 0 if False
""" """
# Check if wien converter was called # Check if wien converter was called
@ -610,7 +608,7 @@ class SumkDFTTools(SumkDFT):
self.read_transport_input_from_hdf() self.read_transport_input_from_hdf()
velocities = self.vk velocities = self.vk
self.n_spin_blocks_input = self.SP + 1 - self.SO n_inequiv_spin_blocks = self.SP + 1 - self.SO # up and down are equivalent if SP = 0
# calculate A(k,w) # calculate A(k,w)
@ -620,7 +618,7 @@ class SumkDFTTools(SumkDFT):
assert self.k_dep_projection == 1, "Not implemented!" assert self.k_dep_projection == 1, "Not implemented!"
# Define mesh for Greens function and the used energy range # Define mesh for Greens function and the used energy range
if (DFT_only == False): if (with_Sigma == False):
self.omega = numpy.array([round(x.real,12) for x in self.Sigma_imp[0].mesh]) self.omega = numpy.array([round(x.real,12) for x in self.Sigma_imp[0].mesh])
mu = self.chemical_potential mu = self.chemical_potential
n_om = len(self.omega) n_om = len(self.omega)
@ -650,8 +648,8 @@ class SumkDFTTools(SumkDFT):
self.omega = numpy.linspace(energywindow[0],energywindow[1],n_om) self.omega = numpy.linspace(energywindow[0],energywindow[1],n_om)
mu = 0.0 mu = 0.0
if (abs(self.fermidis(self.omega[0]*beta)*self.fermidis(-self.omega[0]*beta)) > 1e-5 if (abs(self.fermi_dis(self.omega[0]*beta)*self.fermi_dis(-self.omega[0]*beta)) > 1e-5
or abs(self.fermidis(self.omega[-1]*beta)*self.fermidis(-self.omega[-1]*beta)) > 1e-5): or abs(self.fermi_dis(self.omega[-1]*beta)*self.fermi_dis(-self.omega[-1]*beta)) > 1e-5):
print "\n##########################################" print "\n##########################################"
print "WARNING: Energywindow might be too narrow!" print "WARNING: Energywindow might be too narrow!"
print "##########################################\n" print "##########################################\n"
@ -680,33 +678,33 @@ class SumkDFTTools(SumkDFT):
ntoi = self.spin_names_to_ind[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)) 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) for isp in range(n_inequiv_spin_blocks) ], make_copies=False)
mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(self.n_spin_blocks_input)] # construct mupat mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(n_inequiv_spin_blocks)] # construct mupat
Annkw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_) for isp in range(self.n_spin_blocks_input)] Annkw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_) for isp in range(n_inequiv_spin_blocks)]
ikarray = numpy.array(range(self.n_k)) ikarray = numpy.array(range(self.n_k))
for ik in mpi.slice_array(ikarray): 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)]) unchangesize = all([ self.n_orbitals[ik][isp] == mupat[isp].shape[0] for isp in range(n_inequiv_spin_blocks)])
if (not unchangesize): if (not unchangesize):
# recontruct green functions. # 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)) 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) for isp in range(n_inequiv_spin_blocks) ], make_copies=False)
# construct mupat # construct mupat
mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(self.n_spin_blocks_input)] mupat = [numpy.identity(self.n_orbitals[ik][isp], numpy.complex_) * mu for isp in range(n_inequiv_spin_blocks)]
#set a temporary array storing spectral functions with band index. Note, usually we should have spin index #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)] Annkw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_) for isp in range(n_inequiv_spin_blocks)]
# get lattice green function # get lattice green function
S << 1*Omega + 1j*broadening S << 1*Omega + 1j*broadening
MS = copy.deepcopy(mupat) MS = copy.deepcopy(mupat)
for ibl in range(self.n_spin_blocks_input): for ibl in range(n_inequiv_spin_blocks):
ind = ntoi[bln[ibl]] ind = ntoi[bln[ibl]]
n_orb = self.n_orbitals[ik][ibl] n_orb = self.n_orbitals[ik][ibl]
MS[ibl] = self.hopping[ik,ind,0:n_orb,0:n_orb].real - mupat[ibl] MS[ibl] = self.hopping[ik,ind,0:n_orb,0:n_orb].real - mupat[ibl]
S -= MS S -= MS
if (DFT_only == False): if (with_Sigma == False):
tmp = S.copy() # init temporary storage tmp = S.copy() # init temporary storage
# form self energy from impurity self energy and double counting term. # form self energy from impurity self energy and double counting term.
stmp = self.add_dc() stmp = self.add_dc()
@ -717,10 +715,10 @@ class SumkDFTTools(SumkDFT):
S.invert() S.invert()
for isp in range(self.n_spin_blocks_input): for isp in range(n_inequiv_spin_blocks):
Annkw[isp].real = -copy.deepcopy(S[self.spin_block_names[self.SO][isp]].data.swapaxes(0,1).swapaxes(1,2)).imag / numpy.pi 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): for isp in range(n_inequiv_spin_blocks):
if(ik%100==0): if(ik%100==0):
print "ik,isp", ik, isp print "ik,isp", ik, isp
kvel = velocities[isp][ik] kvel = velocities[isp][ik]
@ -788,55 +786,60 @@ class SumkDFTTools(SumkDFT):
volcc, volpc = self.cellvolume(self.latticetype, self.latticeconstants, self.latticeangles) volcc, volpc = self.cellvolume(self.latticetype, self.latticeconstants, self.latticeangles)
L1,L2,L3= self.Pw_optic.shape n_direction,n_q,n_w= self.Pw_optic.shape
omegaT = self.omega * beta omegaT = self.omega * beta
A0 = numpy.empty((L1,L2), dtype=numpy.float_) A0 = numpy.empty((n_direction,n_q), dtype=numpy.float_)
q_0 = False q_0 = False
Seebeck = numpy.zeros((L1, 1), dtype=numpy.float_) seebeck = numpy.zeros((n_direction, 1), dtype=numpy.float_)
Seebeck[:] = numpy.NAN seebeck[:] = numpy.NAN
d_omega = self.omega[1] - self.omega[0] d_omega = self.omega[1] - self.omega[0]
for iq in xrange(L2): for iq in xrange(n_q):
# treat q = 0, caclulate conductivity and seebeck # treat q = 0, caclulate conductivity and seebeck
if (self.Om_meshr[iq] == 0.0): if (self.Om_meshr[iq] == 0.0):
# if Om_meshr contains multiple entries with w=0, A1 is overwritten! # if Om_meshr contains multiple entries with w=0, A1 is overwritten!
q_0 = True q_0 = True
A1 = numpy.zeros((L1, 1), dtype=numpy.float_) A1 = numpy.zeros((n_direction, 1), dtype=numpy.float_)
for im in xrange(L1): for im in xrange(n_direction):
for iw in xrange(L3): for iw in xrange(n_w):
A0[im, iq] += beta * self.Pw_optic[im, iq, iw] * self.fermidis(omegaT[iw]) * self.fermidis(-omegaT[iw]) A0[im, iq] += beta * self.Pw_optic[im, iq, iw] * self.fermi_dis(omegaT[iw]) * self.fermi_dis(-omegaT[iw])
A1[im] += beta * self.Pw_optic[im, iq, iw] * self.fermidis(omegaT[iw]) * self.fermidis(-omegaT[iw]) * numpy.float(omegaT[iw]) A1[im] += beta * self.Pw_optic[im, iq, iw] * self.fermi_dis(omegaT[iw]) * self.fermi_dis(-omegaT[iw]) * numpy.float(omegaT[iw])
Seebeck[im] = -A1[im] / A0[im, iq] seebeck[im] = -A1[im] / A0[im, iq]
print "A0", A0[im, iq] *d_omega/beta print "A0", A0[im, iq] *d_omega/beta
print "A1", A1[im, iq] *d_omega/beta print "A1", A1[im, iq] *d_omega/beta
# treat q ~= 0, calculate optical conductivity # treat q ~= 0, calculate optical conductivity
else: else:
for im in xrange(L1): for im in xrange(n_direction):
for iw in xrange(L3): for iw in xrange(n_w):
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[im, iq] += self.Pw_optic[im, iq, iw] * (self.fermi_dis(omegaT[iw]) - self.fermi_dis(omegaT[iw] + self.Om_meshr[iq] * beta)) / self.Om_meshr[iq]
A0 *= d_omega A0 *= d_omega
#cond = beta * self.tdintegral(beta, 0)[index] #cond = beta * self.tdintegral(beta, 0)[index]
print "V in bohr^3 ", volpc print "V in bohr^3 ", volpc
# transform to standard unit as in resistivity # transform to standard unit as in resistivity
OpticCon = A0 * 10700.0 / volpc optic_cond = A0 * 10700.0 / volpc
Seebeck *= 86.17 seebeck *= 86.17
# print # print
for im in xrange(L1): for im in xrange(n_direction):
for iq in xrange(L2): for iq in xrange(n_q):
print "Conductivity in direction %s for Om_mesh %d %.4f x 10^4 Ohm^-1 cm^-1" % (self.dir_list[im], iq, OpticCon[im, iq]) print "Conductivity in direction %s for Om_mesh %d %.4f x 10^4 Ohm^-1 cm^-1" % (self.dir_list[im], iq, optic_cond[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]) print "Resistivity in direction %s for Om_mesh %d %.4f x 10^-4 Ohm cm" % (self.dir_list[im], iq, 1.0 / optic_cond[im, iq])
if q_0: if q_0:
print "Seebeck in direction %s for q = 0 %.4f x 10^(-6) V/K" % (self.dir_list[im], Seebeck[im]) 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') ar = HDFArchive(self.hdf_file, 'a')
if not (res_subgrp in ar): ar.create_group(res_subgrp) if not (res_subgrp in ar): ar.create_group(res_subgrp)
things_to_save = ['Seebeck', 'OpticCon'] things_to_save = ['seebeck', 'optic_cond']
for it in things_to_save: ar[res_subgrp][it] = locals()[it] for it in things_to_save: ar[res_subgrp][it] = locals()[it]
ar[res_subgrp]['Seebeck'] = Seebeck ar[res_subgrp]['seebeck'] = seebeck
ar[res_subgrp]['OpticCon'] = OpticCon ar[res_subgrp]['optic_cond'] = optic_cond
del ar del ar
return OpticCon, Seebeck return optic_cond, seebeck
def fermi_dis(self, x):
return 1.0/(numpy.exp(x)+1)

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test/srvo3_transp.output.h5
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test/srvo3_transp.py
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@ -38,6 +38,6 @@ Sigma = ar['dmft_transp_output']['Sigma']
SK.put_Sigma(Sigma_imp = [Sigma]) SK.put_Sigma(Sigma_imp = [Sigma])
del ar del ar
SK.transport_distribution(dir_list=[(0,0)], broadening=0.0, energywindow=[-0.3,0.3], Om_mesh=[0.00, 0.02] , beta=beta, DFT_only=False, save_hdf=False) SK.transport_distribution(dir_list=[(0,0)], broadening=0.0, energywindow=[-0.3,0.3], Om_mesh=[0.00, 0.02] , beta=beta, with_Sigma=False, save_hdf=False)
SK.hdf_file = 'srvo3_transp.output.h5' SK.hdf_file = 'srvo3_transp.output.h5'
SK.conductivity_and_seebeck(beta=beta, read_hdf=False, res_subgrp='results') SK.conductivity_and_seebeck(beta=beta, read_hdf=False, res_subgrp='results')