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https://github.com/triqs/dft_tools
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Some changes in the usage of build_sigma_from_txt.
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Manuel Zingl
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61747745f4
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cf7628065b
@ -47,15 +47,12 @@ You may also have your self energy stored in text files. For this case we provid
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:meth:`constr_Sigma_real_axis`, which loads the data and puts it into a real frequency :class:`BlockGf <pytriqs.gf.local.BlockGf>` object::
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from pytriqs.applications.dft.build_sigma_from_txt import *
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SigmaReFreq = constr_Sigma_real_axis(SK, filename, hdf=False, hdf_dataset='SigmaReFreq',n_om=0, orb=0)
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SigmaReFreq = constr_Sigma_real_axis(filename=filename, gf_struct_orb=SK.gf_struct_solver[0])
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where:
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* `filename`: the name of the hdf5 archive file or the `fname` pattern in text files names as described above,
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* `hdf`: if `True`, the real axis self energy will be read from the hdf5 file, otherwise from the text files,
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* `hdf_dataset`: the name of dataset where the self energy is stored in the hdf5 file,
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* `orb`: index of an inequivalent shell,
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* `n_om`: the number of points in the real-axis mesh (used only if `hdf=False`).
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* `filename`: the `fname` pattern in text files names as described below,
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* `gf_struct_orb`: the Greens function structure for the regarding inequivalent shell.
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It is important that you follow some rules concerning the structure of your data files:
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* Each data file should contain three columns: real frequency, real part and imaginary part of the self energy exactly in this order.
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@ -3,101 +3,74 @@ import string
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from pytriqs.gf.local import *
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def read_fortran_file (filename):
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""" Returns a generator that yields all numbers in the Fortran file as float, one by one"""
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"""Returns a generator that yields all numbers in the Fortran file as float, one by one"""
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import os.path
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if not(os.path.exists(filename)) : raise IOError, "File %s does not exist."%filename
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for line in open(filename,'r') :
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for x in line.replace('D','E').split() :
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yield string.atof(x)
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def constr_Sigma_real_axis(self, filename, hdf=True, hdf_dataset='SigmaReFreq',n_om=0,orb=0, tol_mesh=1e-6):
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def line_count(fname):
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"""Counts the lines of a file"""
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with open(fname) as f:
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for i, l in enumerate(f):
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pass
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return i + 1
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def constr_Sigma_real_axis(filename, gf_struct_orb, tol_mesh=1e-6):
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"""Uses Data from files to construct Sigma (or GF) on the real axis."""
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if not hdf: # then read sigma from text files
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# first get the mesh out of any one of the files:
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bl = self.gf_struct_solver[orb].items()[0][0] # block name
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ol = self.gf_struct_solver[orb].items()[0][1] # list of orbital indices
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if (len(ol)==1): # if blocks are of size one
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Fname = filename+'_'+bl+'.dat'
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else:
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print 'TEST'
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Fname = filename+'_'+bl+'/'+str(ol[0])+'_'+str(ol[0])+'.dat'
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# first get the mesh out of any one of the files:
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bl = gf_struct_orb.items()[0][0] # block name
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ol = gf_struct_orb.items()[0][1] # list of orbital indices
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if (len(ol)==1): # if blocks are of size one
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Fname = filename+'_'+bl+'.dat'
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else:
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Fname = filename+'_'+bl+'/'+str(ol[0])+'_'+str(ol[0])+'.dat'
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try:
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n_om = line_count(Fname)
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R = read_fortran_file(Fname)
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mesh = numpy.zeros([n_om],numpy.float_)
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try:
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for i in xrange(n_om):
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mesh[i] = R.next()
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sk = R.next()
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sk = R.next()
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except StopIteration : # a more explicit error if the file is corrupted.
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raise "SumkDFT.read_Sigma_ME : reading mesh failed!"
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R.close()
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# check whether the mesh is uniform
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bin = (mesh[n_om-1]-mesh[0])/(n_om-1)
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for i in xrange(n_om):
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assert abs(i*bin+mesh[0]-mesh[i]) < tol_mesh, 'constr_Sigma_ME: real-axis mesh is non-uniform!'
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mesh[i] = R.next()
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sk = R.next()
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sk = R.next()
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# construct Sigma
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a_list = [a for a,al in self.gf_struct_solver[orb].iteritems()]
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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()]
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SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
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except StopIteration : # a more explicit error if the file is corrupted.
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raise "constr_Sigma_real_axis : reading mesh failed!"
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R.close()
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#read Sigma
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for i,g in SigmaME:
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mesh=[w for w in g.mesh]
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for iL in g.indices:
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for iR in g.indices:
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if (len(g.indices) == 1):
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Fname = filename+'_%s'%(i)+'.dat'
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else:
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Fname = 'SigmaME_'+'%s'%(i)+'_%s'%(iL)+'_%s'%(iR)+'.dat'
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R = read_fortran_file(Fname)
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try:
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for iom in xrange(n_om):
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sk = R.next()
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rsig = R.next()
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isig = R.next()
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g.data[iom,iL,iR]=rsig+1j*isig
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except StopIteration : # a more explicit error if the file is corrupted.
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raise "SumkDFT.read_Sigma_ME : reading Sigma from file failed!"
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R.close()
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# check whether the mesh is uniform
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bin = (mesh[n_om-1]-mesh[0])/(n_om-1)
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for i in xrange(n_om):
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assert abs(i*bin+mesh[0]-mesh[i]) < tol_mesh, 'constr_Sigma_real_axis: real-axis mesh is non-uniform!'
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# construct Sigma
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a_list = [a for a,al in gf_struct_orb.iteritems()]
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glist = lambda : [ GfReFreq(indices = al, window=(mesh[0],mesh[n_om-1]),n_points=n_om) for a,al in gf_struct_orb.iteritems()]
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SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
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else: # read sigma from hdf
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omega_min=0.0
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omega_max=0.0
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n_om=0
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if (mpi.is_master_node()):
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ar = HDFArchive(filename)
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SigmaME = ar[hdf_dataset]
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del ar
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#OTHER SOLUTION FIXME
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#else:
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# SigmaME=0
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#SigmaME = mpi.broadcast..
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# we need some parameters to construct Sigma on other nodes
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omega_min=SigmaME.mesh.omega_min
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omega_max=SigmaME.mesh.omega_max
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n_om=len(SigmaME.mesh)
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omega_min=mpi.bcast(omega_min)
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omega_max=mpi.bcast(omega_max)
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n_om=mpi.bcast(n_om)
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mpi.barrier()
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# construct Sigma on other nodes
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if (not mpi.is_master_node()):
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a_list = [a for a,al in self.gf_struct_solver[orb].iteritems()]
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glist = lambda : [ GfReFreq(indices = al, window=(omega_min,omega_max),n_points=n_om) for a,al in self.gf_struct_solver[orb].iteritems()]
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SigmaME = BlockGf(name_list = a_list, block_list = glist(),make_copies=False)
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# pass SigmaME to other nodes
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SigmaME = mpi.bcast(SigmaME)
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mpi.barrier()
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#read Sigma
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for i,g in SigmaME:
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mesh=[w for w in g.mesh]
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for iL in g.indices:
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for iR in g.indices:
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if (len(g.indices) == 1):
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Fname = filename+'_%s'%(i)+'.dat'
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else:
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Fname = 'SigmaME_'+'%s'%(i)+'_%s'%(iL)+'_%s'%(iR)+'.dat'
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R = read_fortran_file(Fname)
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try:
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for iom in xrange(n_om):
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sk = R.next()
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rsig = R.next()
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isig = R.next()
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g.data[iom,iL,iR]=rsig+1j*isig
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except StopIteration : # a more explicit error if the file is corrupted.
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raise "constr_Sigma_real_axis : reading Sigma from file failed!"
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R.close()
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SigmaME.note='ReFreq'
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@ -19,7 +19,7 @@ for name, s in Sigma_hdf:
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# Read self energy from txt files
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SK = SumkDFTTools(hdf_file = 'SrVO3.h5', use_dft_blocks = True)
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Sigma_txt = constr_Sigma_real_axis(SK, 'Sigma', hdf=False, n_om=101, orb=0)
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Sigma_txt = constr_Sigma_real_axis(filename='Sigma', gf_struct_orb=SK.gf_struct_solver[0])
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SK.put_Sigma(Sigma_imp = [Sigma_txt])
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SK.hdf_file = 'sigma_from_file.output.h5'
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