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Tidy up of symmetry

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*changed map -> orb_map in symmetry to avoid using python keyword
This commit is contained in:
Priyanka Seth 2014-11-14 18:13:43 +01:00
parent 628f774234
commit b672839f83
6 changed files with 54 additions and 63 deletions
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1
python/TODOFIX
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@ -8,6 +8,7 @@ Substitutions:
* read_symmetry_input -> convert_symmetry_input
* Symm_corr -> symmcorr
* gf_struct_corr -> gf_struct_sumk
* n_s -> n_symm
internal substitutions:
Symm_par --> symmpar

16
python/converters/wien2k_converter.py
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@ -374,26 +374,26 @@ class Wien2kConverter(ConverterTools):
R = ConverterTools.read_fortran_file(self,symm_file,self.fortran_to_replace)
try:
n_s = int(R.next()) # Number of symmetry operations
n_symm = int(R.next()) # Number of symmetry operations
n_atoms = int(R.next()) # number of atoms involved
perm = [ [int(R.next()) for i in xrange(n_atoms)] for j in xrange(n_s) ] # list of permutations of the atoms
perm = [ [int(R.next()) for i in xrange(n_atoms)] for j in xrange(n_symm) ] # list of permutations of the atoms
if SP:
time_inv = [ int(R.next()) for j in xrange(n_s) ] # timeinversion for SO xoupling
time_inv = [ int(R.next()) for j in xrange(n_symm) ] # time inversion for SO coupling
else:
time_inv = [ 0 for j in xrange(n_s) ]
time_inv = [ 0 for j in xrange(n_symm) ]
# Now read matrices:
mat = []
for in_s in xrange(n_s):
for i_symm in xrange(n_symm):
mat.append( [ numpy.zeros([orbits[orb][3], orbits[orb][3]],numpy.complex_) for orb in xrange(n_orbits) ] )
for orb in range(n_orbits):
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat[in_s][orb][i,j] = R.next() # real part
mat[i_symm][orb][i,j] = R.next() # real part
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat[in_s][orb][i,j] += 1j * R.next() # imaginary part
mat[i_symm][orb][i,j] += 1j * R.next() # imaginary part
mat_tinv = [numpy.identity(orbits[orb][3],numpy.complex_)
for orb in range(n_orbits)]
@ -419,6 +419,6 @@ class Wien2kConverter(ConverterTools):
# Save it to the HDF:
ar=HDFArchive(self.hdf_file,'a')
if not (symm_subgrp in ar): ar.create_group(symm_subgrp)
things_to_save = ['n_s','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
things_to_save = ['n_symm','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

90
python/symmetry.py
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@ -20,15 +20,12 @@
#
################################################################################
import copy,numpy
import string
from types import *
from pytriqs.gf.local import *
from pytriqs.archive import *
import pytriqs.utility.mpi as mpi
class Symmetry:
"""This class provides the routines for applying symmetry operations for the k sums.
It contains the permutations of the atoms in the unti cell, and the corresponding
@ -38,18 +35,19 @@ class Symmetry:
"""Initialises the class.
Reads the permutations and rotation matrizes from the file, and constructs the mapping for
the given orbitals. For each orbit a matrix is read!!!
SO: Flag for SO coupled calculations.
SP: Spin polarisation yes/no
SO: Flag for spin-orbit coupling.
SP: Flag for spin polarisation.
"""
assert type(hdf_file)==StringType,"hdf_file must be a filename"; self.hdf_file = hdf_file
things_to_read = ['n_s','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
assert type(hdf_file) == StringType, "hdf_file must be a filename"
self.hdf_file = hdf_file
things_to_read = ['n_symm','n_atoms','perm','orbits','SO','SP','time_inv','mat','mat_tinv']
for it in things_to_read: setattr(self,it,0)
if (mpi.is_master_node()):
if mpi.is_master_node():
#Read the stuff on master:
ar = HDFArchive(hdf_file,'a')
if (subgroup is None):
if subgroup is None:
ar2 = ar
else:
ar2 = ar[subgroup]
@ -62,81 +60,68 @@ class Symmetry:
for it in things_to_read: setattr(self,it,mpi.bcast(getattr(self,it)))
# now define the mapping of orbitals:
# self.map[iorb]=jorb gives the permutation of the orbitals as given in the list, when the
# self.orb_map[iorb] = jorb gives the permutation of the orbitals as given in the list, when the
# permutation of the atoms is done:
self.n_orbits = len(self.orbits)
self.map = [ [0 for iorb in range(self.n_orbits)] for in_s in range(self.n_s) ]
for in_s in range(self.n_s):
self.orb_map = [ [0 for iorb in range(self.n_orbits)] for i_symm in range(self.n_symm) ]
for i_symm in range(self.n_symm):
for iorb in range(self.n_orbits):
srch = copy.deepcopy(self.orbits[iorb])
srch[0] = self.perm[in_s][self.orbits[iorb][0]-1]
self.map[in_s][iorb] = self.orbits.index(srch)
srch[0] = self.perm[i_symm][self.orbits[iorb][0]-1]
self.orb_map[i_symm][iorb] = self.orbits.index(srch)
def symmetrize(self,obj):
assert isinstance(obj,list),"obj has to be a list of objects!"
assert len(obj)==self.n_orbits,"obj has to be a list of the same length as defined in the init"
assert isinstance(obj,list), "symmetry: obj has to be a list of objects."
assert len(obj) == self.n_orbits, "symmetry: obj has to be a list of the same length as defined in the init."
if (isinstance(obj[0],BlockGf)):
if isinstance(obj[0],BlockGf):
symm_obj = [ obj[i].copy() for i in range(len(obj)) ] # here the result is stored, it is a BlockGf!
for iorb in range(self.n_orbits): symm_obj[iorb].zero() # set to zero
else:
# if not a BlockGf, we assume it is a matrix (density matrix), has to be complex since self.mat is complex!
#symm_obj = [ numpy.zeros([self.orbits[iorb][3],self.orbits[iorb][3]],numpy.complex_) for iorb in range(self.n_orbits) ]
symm_obj = [ copy.deepcopy(obj[i]) for i in range(len(obj)) ]
for iorb in range(self.n_orbits):
if (type(symm_obj[iorb])==DictType):
if type(symm_obj[iorb]) == DictType:
for ii in symm_obj[iorb]: symm_obj[iorb][ii] *= 0.0
else:
symm_obj[iorb] *= 0.0
for in_s in range(self.n_s):
for i_symm in range(self.n_symm):
for iorb in range(self.n_orbits):
l = self.orbits[iorb][2] # s, p, d, or f
dim = self.orbits[iorb][3]
jorb = self.map[in_s][iorb]
jorb = self.orb_map[i_symm][iorb]
if (isinstance(obj[0],BlockGf)):
if isinstance(obj[0],BlockGf):
tmp = obj[iorb].copy()
if (self.time_inv[in_s]): tmp << tmp.transpose()
for bname,gf in tmp: tmp[bname].from_L_G_R(self.mat[in_s][iorb],tmp[bname],self.mat[in_s][iorb].conjugate().transpose())
tmp *= 1.0/self.n_s
if self.time_inv[i_symm]: tmp << tmp.transpose()
for bname,gf in tmp: tmp[bname].from_L_G_R(self.mat[i_symm][iorb],tmp[bname],self.mat[i_symm][iorb].conjugate().transpose())
tmp *= 1.0/self.n_symm
symm_obj[jorb] += tmp
else:
if (type(obj[iorb])==DictType):
if type(obj[iorb]) == DictType:
for ii in obj[iorb]:
if (self.time_inv[in_s]==0):
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[in_s][iorb],obj[iorb][ii]),
self.mat[in_s][iorb].conjugate().transpose()) / self.n_s
if self.time_inv[i_symm] == 0:
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb][ii]),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
else:
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[in_s][iorb],obj[iorb][ii].conjugate()),
self.mat[in_s][iorb].conjugate().transpose()) / self.n_s
symm_obj[jorb][ii] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb][ii].conjugate()),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
else:
if (self.time_inv[in_s]==0):
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[in_s][iorb],obj[iorb]),self.mat[in_s][iorb].conjugate().transpose()) / self.n_s
if self.time_inv[i_symm] == 0:
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb]),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
else:
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[in_s][iorb],obj[iorb].conjugate()),
self.mat[in_s][iorb].conjugate().transpose()) / self.n_s
symm_obj[jorb] += numpy.dot(numpy.dot(self.mat[i_symm][iorb],obj[iorb].conjugate()),
self.mat[i_symm][iorb].conjugate().transpose()) / self.n_symm
# Markus: This does not what it is supposed to do, check how this should work (keep for now)
# if ((self.SO==0) and (self.SP==0)):
# if (self.SO == 0) and (self.SP == 0):
# # add time inv:
#mpi.report("Add time inversion")
# for iorb in range(self.n_orbits):
@ -148,7 +133,7 @@ class Symmetry:
# symm_obj[iorb] /= 2.0
#
# else:
# if (type(symm_obj[iorb])==DictType):
# if type(symm_obj[iorb]) == DictType:
# for ii in symm_obj[iorb]:
# symm_obj[iorb][ii] += numpy.dot(numpy.dot(self.mat_tinv[iorb],symm_obj[iorb][ii].conjugate()),
# self.mat_tinv[iorb].transpose().conjugate())
@ -158,9 +143,4 @@ class Symmetry:
# self.mat_tinv[iorb].transpose().conjugate())
# symm_obj[iorb] /= 2.0
return symm_obj

10
python/update_archive.py
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@ -17,6 +17,7 @@ If you encounter any problem please report it on github!
filename = sys.argv[1]
A = h5py.File(filename)
# Rename groups
old_to_new = {'SumK_LDA':'lda_input', 'SumK_LDA_ParProj':'lda_parproj_input',
'SymmCorr':'lda_symmcorr_input', 'SymmPar':'lda_symmpar_input', 'SumK_LDA_Bands':'lda_bands_input'}
@ -26,6 +27,7 @@ for old, new in old_to_new.iteritems():
A.copy(old,new)
del(A[old])
# Move output items from lda_input to lda_output
move_to_output = ['gf_struct_solver','map_inv','map',
'chemical_potential','dc_imp','dc_energ','deg_shells',
'h_field']
@ -36,6 +38,14 @@ for obj in move_to_output:
A.copy('lda_input/'+obj,'lda_output/'+obj)
del(A['lda_input'][obj])
# Rename variables
groups = ['lda_symmcorr_input','lda_symmpar_input']
for group in groups:
if group not in A.keys(): continue
print "Changing n_s to n_symm ..."
A[group].move('n_s','n_symm')
A.close()
# Repack to reclaim disk space

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test/SrVO3.h5
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test/wien2k_convert.output.h5
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