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Some changes in the usage of build_sigma_from_txt.

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Manuel Zingl 2015-08-24 14:47:08 +02:00
parent 61747745f4
commit cf7628065b
3 changed files with 55 additions and 85 deletions
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9
doc/guide/analysis.rst
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@ -47,15 +47,12 @@ You may also have your self energy stored in text files. For this case we provid
:meth:`constr_Sigma_real_axis`, which loads the data and puts it into a real frequency :class:`BlockGf <pytriqs.gf.local.BlockGf>` object::
from pytriqs.applications.dft.build_sigma_from_txt import *
SigmaReFreq = constr_Sigma_real_axis(SK, filename, hdf=False, hdf_dataset='SigmaReFreq',n_om=0, orb=0)
SigmaReFreq = constr_Sigma_real_axis(filename=filename, gf_struct_orb=SK.gf_struct_solver[0])
where:
* `filename`: the name of the hdf5 archive file or the `fname` pattern in text files names as described above,
* `hdf`: if `True`, the real axis self energy will be read from the hdf5 file, otherwise from the text files,
* `hdf_dataset`: the name of dataset where the self energy is stored in the hdf5 file,
* `orb`: index of an inequivalent shell,
* `n_om`: the number of points in the real-axis mesh (used only if `hdf=False`).
* `filename`: the `fname` pattern in text files names as described below,
* `gf_struct_orb`: the Greens function structure for the regarding inequivalent shell.
It is important that you follow some rules concerning the structure of your data files:
* Each data file should contain three columns: real frequency, real part and imaginary part of the self energy exactly in this order.

65
python/build_sigma_from_txt.py
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@ -3,47 +3,53 @@ import string
from pytriqs.gf.local import *
def read_fortran_file (filename):
""" Returns a generator that yields all numbers in the Fortran file as float, one by one"""
"""Returns a generator that yields all numbers in the Fortran file as float, one by one"""
import os.path
if not(os.path.exists(filename)) : raise IOError, "File %s does not exist."%filename
for line in open(filename,'r') :
for x in line.replace('D','E').split() :
yield string.atof(x)
def constr_Sigma_real_axis(self, filename, hdf=True, hdf_dataset='SigmaReFreq',n_om=0,orb=0, tol_mesh=1e-6):
def line_count(fname):
"""Counts the lines of a file"""
with open(fname) as f:
for i, l in enumerate(f):
pass
return i + 1
def constr_Sigma_real_axis(filename, gf_struct_orb, tol_mesh=1e-6):
"""Uses Data from files to construct Sigma (or GF) on the real axis."""
if not hdf: # then read sigma from text files
# first get the mesh out of any one of the files:
bl = self.gf_struct_solver[orb].items()[0][0] # block name
ol = self.gf_struct_solver[orb].items()[0][1] # list of orbital indices
bl = gf_struct_orb.items()[0][0] # block name
ol = gf_struct_orb.items()[0][1] # list of orbital indices
if (len(ol)==1): # if blocks are of size one
Fname = filename+'_'+bl+'.dat'
else:
print 'TEST'
Fname = filename+'_'+bl+'/'+str(ol[0])+'_'+str(ol[0])+'.dat'
try:
n_om = line_count(Fname)
R = read_fortran_file(Fname)
mesh = numpy.zeros([n_om],numpy.float_)
try:
for i in xrange(n_om):
mesh[i] = R.next()
sk = R.next()
sk = R.next()
except StopIteration : # a more explicit error if the file is corrupted.
raise "SumkDFT.read_Sigma_ME : reading mesh failed!"
raise "constr_Sigma_real_axis : reading mesh failed!"
R.close()
# check whether the mesh is uniform
bin = (mesh[n_om-1]-mesh[0])/(n_om-1)
for i in xrange(n_om):
assert abs(i*bin+mesh[0]-mesh[i]) < tol_mesh, 'constr_Sigma_ME: real-axis mesh is non-uniform!'
assert abs(i*bin+mesh[0]-mesh[i]) < tol_mesh, 'constr_Sigma_real_axis: real-axis mesh is non-uniform!'
# construct Sigma
a_list = [a for a,al in self.gf_struct_solver[orb].iteritems()]
glist = lambda : [ GfReFreq(indices = al, window=(mesh[0],mesh[n_om-1]),n_points=n_om) for a,al in self.gf_struct_solver[orb].iteritems()]
a_list = [a for a,al in gf_struct_orb.iteritems()]
glist = lambda : [ GfReFreq(indices = al, window=(mesh[0],mesh[n_om-1]),n_points=n_om) for a,al in gf_struct_orb.iteritems()]
SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
#read Sigma
@ -63,42 +69,9 @@ def constr_Sigma_real_axis(self, filename, hdf=True, hdf_dataset='SigmaReFreq',n
isig = R.next()
g.data[iom,iL,iR]=rsig+1j*isig
except StopIteration : # a more explicit error if the file is corrupted.
raise "SumkDFT.read_Sigma_ME : reading Sigma from file failed!"
raise "constr_Sigma_real_axis : reading Sigma from file failed!"
R.close()
else: # read sigma from hdf
omega_min=0.0
omega_max=0.0
n_om=0
if (mpi.is_master_node()):
ar = HDFArchive(filename)
SigmaME = ar[hdf_dataset]
del ar
#OTHER SOLUTION FIXME
#else:
# SigmaME=0
#SigmaME = mpi.broadcast..
# we need some parameters to construct Sigma on other nodes
omega_min=SigmaME.mesh.omega_min
omega_max=SigmaME.mesh.omega_max
n_om=len(SigmaME.mesh)
omega_min=mpi.bcast(omega_min)
omega_max=mpi.bcast(omega_max)
n_om=mpi.bcast(n_om)
mpi.barrier()
# construct Sigma on other nodes
if (not mpi.is_master_node()):
a_list = [a for a,al in self.gf_struct_solver[orb].iteritems()]
glist = lambda : [ GfReFreq(indices = al, window=(omega_min,omega_max),n_points=n_om) for a,al in self.gf_struct_solver[orb].iteritems()]
SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
# pass SigmaME to other nodes
SigmaME = mpi.bcast(SigmaME)
mpi.barrier()
SigmaME.note='ReFreq'
return SigmaME

2
test/sigma_from_file.py
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@ -19,7 +19,7 @@ for name, s in Sigma_hdf:
# Read self energy from txt files
SK = SumkDFTTools(hdf_file = 'SrVO3.h5', use_dft_blocks = True)
Sigma_txt = constr_Sigma_real_axis(SK, 'Sigma', hdf=False, n_om=101, orb=0)
Sigma_txt = constr_Sigma_real_axis(filename='Sigma', gf_struct_orb=SK.gf_struct_solver[0])
SK.put_Sigma(Sigma_imp = [Sigma_txt])
SK.hdf_file = 'sigma_from_file.output.h5'