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Move repeated converter functions in converter_tools.py

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This commit is contained in:
Priyanka Seth 2014-11-08 23:51:24 +01:00
parent 0bb1a45afb
commit a7f2a5096f
4 changed files with 96 additions and 134 deletions
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2
python/TODOFIX
View File

@ -35,6 +35,8 @@ par_proj_data -> parproj_data
symm_par_data -> symmpar_data
**********
* separated read_fortran_file, __repack, inequiv_shells into new converter_tools class from which hk and wien converters are derived
* moved find_dc, find_mu_nonint, check_projectors, sorts_of_atoms,
number_of_atoms to end, not to be documented.

78
python/converters/converter_tools.py Normal file
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@ -0,0 +1,78 @@
################################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
# Copyright (C) 2011 by M. Aichhorn
#
# TRIQS is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
class ConverterTools:
def read_fortran_file(self,filename,to_replace):
""" Returns a generator that yields all numbers in the Fortran file as float, one by one"""
import os.path
import string
if not(os.path.exists(filename)) : raise IOError, "File %s does not exist."%filename
for line in open(filename,'r') :
for old,new in to_replace.iteritems(): line = line.replace(old,new)
for x in line.split(): yield string.atof(x)
def __repack(self):
"""Calls the h5repack routine, in order to reduce the file size of the hdf5 archive.
Should only be used BEFORE the first invokation of HDFArchive in the program, otherwise
the hdf5 linking is broken!!!"""
import subprocess
if not (mpi.is_master_node()): return
mpi.report("Repacking the file %s"%self.hdf_file)
retcode = subprocess.call(["h5repack","-i%s"%self.hdf_file, "-otemphgfrt.h5"])
if (retcode!=0):
mpi.report("h5repack failed!")
else:
subprocess.call(["mv","-f","temphgfrt.h5","%s"%self.hdf_file])
def inequiv_shells(self,lst):
"""
The number of inequivalent shells is calculated from lst, and a mapping is given as
map(i_corr_shells) = i_inequiv_corr_shells
invmap(i_inequiv_corr_shells) = i_corr_shells
in order to put the self energies to all equivalent shells, and for extracting Gloc
"""
tmp = []
self.shellmap = [0 for i in range(len(lst))]
self.invshellmap = [0]
self.n_inequiv_corr_shells = 1
tmp.append( lst[0][1:3] )
if (len(lst)>1):
for i in range(len(lst)-1):
fnd = False
for j in range(self.n_inequiv_corr_shells):
if (tmp[j]==lst[i+1][1:3]):
fnd = True
self.shellmap[i+1] = j
if (fnd==False):
self.shellmap[i+1] = self.n_inequiv_corr_shells
self.n_inequiv_corr_shells += 1
tmp.append( lst[i+1][1:3] )
self.invshellmap.append(i+1)

73
python/converters/hk_converter.py
View File

@ -24,21 +24,10 @@ from types import *
import numpy
from pytriqs.archive import *
import pytriqs.utility.mpi as mpi
import string
from math import sqrt
from converter_tools import *
def read_fortran_file (filename):
""" 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').replace('(',' ').replace(')',' ').replace(',',' ').split() :
yield string.atof(x)
class HkConverter:
class HkConverter(ConverterTools):
"""
Conversion from general H(k) file to an hdf5 file that can be used as input for the SumK_LDA class.
"""
@ -46,7 +35,6 @@ class HkConverter:
def __init__(self, hk_file, hdf_file, lda_subgrp = 'lda_input', symmcorr_subgrp = 'lda_symmcorr_input', repacking = False):
"""
Init of the class.
on.
"""
assert type(hk_file)==StringType,"hk_file must be a filename"
@ -54,11 +42,12 @@ class HkConverter:
self.lda_file = hk_file
self.lda_subgrp = lda_subgrp
self.symmcorr_subgrp = symmcorr_subgrp
self.fortran_to_replace = {'D':'E', '(':' ', ')':' ', ',':' '}
# Checks if h5 file is there and repacks it if wanted:
import os.path
if (os.path.exists(self.hdf_file) and repacking):
self.__repack()
ConverterTools.__repack(self)
def convert_dmft_input(self, first_real_part_matrix = True, only_upper_triangle = False, weights_in_file = False):
@ -71,7 +60,7 @@ class HkConverter:
mpi.report("Reading input from %s..."%self.lda_file)
# R is a generator : each R.Next() will return the next number in the file
R = read_fortran_file(self.lda_file)
R = ConverterTools.read_fortran_file(self,self.lda_file,self.fortran_to_replace)
try:
energy_unit = 1.0 # the energy conversion factor is 1.0, we assume eV in files
n_k = int(R.next()) # read the number of k points
@ -93,7 +82,7 @@ class HkConverter:
# now read the information about the shells:
corr_shells = [ [ int(R.next()) for i in range(6) ] for icrsh in range(n_corr_shells) ] # reads iatom, sort, l, dim, SO flag, irep
self.inequiv_shells(corr_shells) # determine the number of inequivalent correlated shells, has to be known for further reading...
ConverterTools.inequiv_shells(self,corr_shells) # determine the number of inequivalent correlated shells, needed for further reading
use_rotations = 0
rot_mat = [numpy.identity(corr_shells[icrsh][3],numpy.complex_) for icrsh in xrange(n_corr_shells)]
@ -210,53 +199,3 @@ class HkConverter:
'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights','hopping']
for it in things_to_save: ar[self.lda_subgrp][it] = locals()[it]
del ar
def __repack(self):
"""Calls the h5repack routine, in order to reduce the file size of the hdf5 archive.
Should only be used BEFORE the first invokation of HDFArchive in the program, otherwise
the hdf5 linking is broken!!!"""
import subprocess
if not (mpi.is_master_node()): return
mpi.report("Repacking the file %s"%self.hdf_file)
retcode = subprocess.call(["h5repack","-i%s"%self.hdf_file, "-otemphgfrt.h5"])
if (retcode!=0):
mpi.report("h5repack failed!")
else:
subprocess.call(["mv","-f","temphgfrt.h5","%s"%self.hdf_file])
def inequiv_shells(self,lst):
"""
The number of inequivalent shells is calculated from lst, and a mapping is given as
map(i_corr_shells) = i_inequiv_corr_shells
invmap(i_inequiv_corr_shells) = i_corr_shells
in order to put the Self energies to all equivalent shells, and for extracting Gloc
"""
tmp = []
self.shellmap = [0 for i in range(len(lst))]
self.invshellmap = [0]
self.n_inequiv_corr_shells = 1
tmp.append( lst[0][1:3] )
if (len(lst)>1):
for i in range(len(lst)-1):
fnd = False
for j in range(self.n_inequiv_corr_shells):
if (tmp[j]==lst[i+1][1:3]):
fnd = True
self.shellmap[i+1] = j
if (fnd==False):
self.shellmap[i+1] = self.n_inequiv_corr_shells
self.n_inequiv_corr_shells += 1
tmp.append( lst[i+1][1:3] )
self.invshellmap.append(i+1)

77
python/converters/wien2k_converter.py
View File

@ -24,20 +24,9 @@ from types import *
import numpy
from pytriqs.archive import *
import pytriqs.utility.mpi as mpi
import string
from converter_tools import *
def read_fortran_file (filename):
""" 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)
class Wien2kConverter:
class Wien2kConverter(ConverterTools):
"""
Conversion from Wien2k output to an hdf5 file that can be used as input for the SumkLDA class.
"""
@ -61,11 +50,12 @@ class Wien2kConverter:
self.parproj_subgrp = parproj_subgrp
self.symmpar_subgrp = symmpar_subgrp
self.bands_subgrp = bands_subgrp
self.fortran_to_replace = {'D':'E'}
# Checks if h5 file is there and repacks it if wanted:
import os.path
if (os.path.exists(self.hdf_file) and repacking):
self.__repack()
ConverterTools.__repack(self)
@ -79,7 +69,7 @@ class Wien2kConverter:
mpi.report("Reading input from %s..."%self.lda_file)
# R is a generator : each R.Next() will return the next number in the file
R = read_fortran_file(self.lda_file)
R = ConverterTools.read_fortran_file(self,self.lda_file,self.fortran_to_replace)
try:
energy_unit = R.next() # read the energy convertion factor
n_k = int(R.next()) # read the number of k points
@ -100,7 +90,7 @@ class Wien2kConverter:
# now read the information about the shells:
corr_shells = [ [ int(R.next()) for i in range(6) ] for icrsh in range(n_corr_shells) ] # reads iatom, sort, l, dim, SO flag, irep
self.inequiv_shells(corr_shells) # determine the number of inequivalent correlated shells, needed for further reading
ConverterTools.inequiv_shells(self,corr_shells) # determine the number of inequivalent correlated shells, needed for further reading
use_rotations = 1
rot_mat = [numpy.identity(corr_shells[icrsh][3],numpy.complex_) for icrsh in xrange(n_corr_shells)]
@ -222,7 +212,7 @@ class Wien2kConverter:
dens_mat_below = [ [numpy.zeros([self.shells[ish][3],self.shells[ish][3]],numpy.complex_) for ish in range(self.n_shells)]
for isp in range(self.n_spin_blocs) ]
R = read_fortran_file(self.parproj_file)
R = ConverterTools.read_fortran_file(self,self.parproj_file,self.fortran_to_replace)
n_parproj = [int(R.next()) for i in range(self.n_shells)]
n_parproj = numpy.array(n_parproj)
@ -295,7 +285,7 @@ class Wien2kConverter:
if not (mpi.is_master_node()): return
mpi.report("Reading bands input from %s..."%self.band_file)
R = read_fortran_file(self.band_file)
R = ConverterTools.read_fortran_file(self,self.band_file,self.fortran_to_replace)
try:
n_k = int(R.next())
@ -380,7 +370,8 @@ class Wien2kConverter:
mpi.report("Reading symmetry input from %s..."%symm_file)
n_orbits = len(orbits)
R=read_fortran_file(symm_file)
R = ConverterTools.read_fortran_file(self,symm_file,self.fortran_to_replace)
try:
n_s = int(R.next()) # Number of symmetry operations
@ -431,51 +422,3 @@ class Wien2kConverter:
things_to_save = ['n_s','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
for it in things_to_save: ar[symm_subgrp][it] = locals()[it]
del ar
def __repack(self):
"""Calls the h5repack routine, in order to reduce the file size of the hdf5 archive.
Should only be used BEFORE the first invokation of HDFArchive in the program, otherwise
the hdf5 linking is broken!!!"""
import subprocess
if not (mpi.is_master_node()): return
mpi.report("Repacking the file %s"%self.hdf_file)
return_code = subprocess.call(["h5repack", "-i %s"%self.hdf_file, "-o temphgfrt.h5"])
if (return_code != 0):
mpi.report("h5repack failed!")
else:
subprocess.call(["mv", "-f", "temphgfrt.h5", "%s"%self.hdf_file])
def inequiv_shells(self,lst):
"""
The number of inequivalent shells is calculated from lst, and a mapping is given as
map(i_corr_shells) = i_inequiv_corr_shells
invmap(i_inequiv_corr_shells) = i_corr_shells
in order to put the Self energies to all equivalent shells, and for extracting Gloc
"""
tmp = []
self.shellmap = [0 for i in range(len(lst))]
self.invshellmap = [0]
self.n_inequiv_corr_shells = 1
tmp.append( lst[0][1:3] )
if (len(lst)>1):
for i in range(len(lst)-1):
fnd = False
for j in range(self.n_inequiv_corr_shells):
if (tmp[j]==lst[i+1][1:3]):
fnd = True
self.shellmap[i+1] = j
if (fnd==False):
self.shellmap[i+1] = self.n_inequiv_corr_shells
self.n_inequiv_corr_shells += 1
tmp.append( lst[i+1][1:3] )
self.invshellmap.append(i+1)