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BlockStructure class for manipulating GF structures

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BlockStructure stores gf_struct_solver and gf_struct_sumk
and the mappings between them. It allows to modify it, and
save it to HDF (see issue #67).
This commit is contained in:
Gernot J. Kraberger 2016-09-13 11:57:48 +02:00
parent d8483a0bb1
commit e4af7dbd1b
9 changed files with 594 additions and 3 deletions
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1
doc/documentation.rst
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@ -45,6 +45,7 @@ This is the reference manual for the python routines.
reference/sumk_dft_tools
reference/symmetry
reference/transbasis
reference/block_structure
FAQs

22
doc/reference/block_structure.rst Normal file
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@ -0,0 +1,22 @@
Block Structure
===============
The `BlockStructure` class allows to change and manipulate
Green's functions structures and mappings from sumk to solver.
The block structure can also be written to and read from HDF files.
.. warning::
Do not write the individual elements of this class to a HDF file,
as they belong together and changing one without the other can
result in unexpected results. Always write the BlockStructure
object as a whole.
Writing the sumk_to_solver and solver_to_sumk elements
individually is not implemented.
.. autoclass:: dft.block_structure.BlockStructure
:members:
:show-inheritance:

3
python/__init__.py
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@ -22,8 +22,9 @@
from sumk_dft import SumkDFT
from symmetry import Symmetry
from block_structure import BlockStructure
from sumk_dft_tools import SumkDFTTools
from converters import *
__all__ = ['SumkDFT', 'Symmetry', 'SumkDFTTools',
'Wien2kConverter', 'HkConverter']
'Wien2kConverter', 'HkConverter','BlockStructure']

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python/block_structure.py Normal file
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@ -0,0 +1,442 @@
import copy
import numpy as np
from pytriqs.gf.local import GfImFreq, BlockGf
from ast import literal_eval
from warnings import warn
class BlockStructure(object):
""" Contains information about the Green function structure.
This class contains information about the structure of the solver
and sumk Green functions and the mapping between them.
Parameters
----------
gf_struct_sumk : list of list of tuple
gf_struct_sumk[ish][idx] = (block_name,list of indices in block)
for correlated shell ish; idx is just a counter in the list
gf_struct_solver : list of dict
gf_struct_solver[ish][block] = list of indices in that block
for *inequivalent* correlated shell ish
solver_to_sumk : list of dict
solver_to_sumk[ish][(from_block,from_idx)] = (to_block,to_idx)
maps from the solver block and index to the sumk block and index
for *inequivalent* correlated shell ish
sumk_to_solver : list of dict
sumk_to_solver[ish][(from_block,from_idx)] = (to_block,to_idx)
maps from the sumk block and index to the solver block and index
for *inequivalent* correlated shell ish
solver_to_sumk_block : list of dict
solver_to_sumk_block[ish][from_block] = to_block
maps from the solver block to the sumk block
for *inequivalent* correlated shell ish
"""
def __init__(self,gf_struct_sumk=None,
gf_struct_solver=None,
solver_to_sumk=None,
sumk_to_solver=None,
solver_to_sumk_block=None):
self.gf_struct_sumk = gf_struct_sumk
self.gf_struct_solver = gf_struct_solver
self.solver_to_sumk = solver_to_sumk
self.sumk_to_solver = sumk_to_solver
self.solver_to_sumk_block = solver_to_sumk_block
@classmethod
def full_structure(cls,gf_struct,corr_to_inequiv):
""" Construct structure that maps to itself.
This has the same structure for sumk and solver, and the
mapping solver_to_sumk and sumk_to_solver is one-to-one.
Parameters
----------
gf_struct : list of dict
gf_struct[ish][block] = list of indices in that block
for (inequivalent) correlated shell ish
corr_to_inequiv : list
gives the mapping from correlated shell csh to inequivalent
correlated shell icsh, so that corr_to_inequiv[csh]=icsh
e.g. SumkDFT.corr_to_inequiv
if None, each inequivalent correlated shell is supposed to
be correspond to just one correlated shell with the same
index; there is not default, None has to be set explicitly!
"""
solver_to_sumk = []
s2sblock = []
gs_sumk = []
for ish in range(len(gf_struct)):
so2su = {}
so2sublock = {}
gss = []
for block in gf_struct[ish]:
so2sublock[block]=block
for ind in gf_struct[ish][block]:
so2su[(block,ind)]=(block,ind)
gss.append((block,gf_struct[ish][block]))
solver_to_sumk.append(so2su)
s2sblock.append(so2sublock)
gs_sumk.append(gss)
# gf_struct_sumk is not given for each inequivalent correlated
# shell, but for every correlated shell!
if corr_to_inequiv is not None:
gs_sumk_all = [None]*len(corr_to_inequiv)
for i in range(len(corr_to_inequiv)):
gs_sumk_all[i] = gs_sumk[corr_to_inequiv[i]]
else:
gs_sumk_all = gs_sumk
return cls(gf_struct_solver=copy.deepcopy(gf_struct),
gf_struct_sumk = gs_sumk_all,
solver_to_sumk = copy.deepcopy(solver_to_sumk),
sumk_to_solver = solver_to_sumk,
solver_to_sumk_block = s2sblock)
def pick_gf_struct_solver(self,new_gf_struct):
""" Pick selected orbitals within blocks.
This throws away parts of the Green's function that (for some
reason - be sure that you know what you're doing) shouldn't be
included in the calculation.
To drop an entire block, just don't include it.
To drop a certain index within a block, just don't include it.
If it was before:
[{'up':[0,1],'down':[0,1],'left':[0,1]}]
to choose the 0th index of the up block and the 1st index of
the down block and drop the left block, the new_gf_struct would
have to be
[{'up':[0],'down':[1]}]
Note that the indices will be renamed to be a 0-based
sequence of integers, i.e. the new structure will actually
be [{'up':[0],'down':[0]}].
For dropped indices, sumk_to_solver will map to (None,None).
Parameters
----------
new_gf_struct : list of dict
formatted the same as gf_struct_solver:
new_gf_struct[ish][block]=list of indices in that block.
"""
for ish in range(len(self.gf_struct_solver)):
gf_struct = new_gf_struct[ish]
# create new solver_to_sumk
so2su={}
so2su_block = {}
for blk,idxs in gf_struct.items():
for i in range(len(idxs)):
so2su[(blk,i)]=self.solver_to_sumk[ish][(blk,idxs[i])]
so2su_block[blk]=so2su[(blk,i)][0]
self.solver_to_sumk[ish] = so2su
self.solver_to_sumk_block[ish] = so2su_block
# create new sumk_to_solver
for k,v in self.sumk_to_solver[ish].items():
blk,ind=v
if blk in gf_struct and ind in gf_struct[blk]:
new_ind = gf_struct[blk].index(ind)
self.sumk_to_solver[ish][k]=(blk,new_ind)
else:
self.sumk_to_solver[ish][k]=(None,None)
# reindexing gf_struct so that it starts with 0
for k in gf_struct:
gf_struct[k]=range(len(gf_struct[k]))
self.gf_struct_solver[ish]=gf_struct
def pick_gf_struct_sumk(self,new_gf_struct):
""" Pick selected orbitals within blocks.
This throws away parts of the Green's function that (for some
reason - be sure that you know what you're doing) shouldn't be
included in the calculation.
To drop an entire block, just don't include it.
To drop a certain index within a block, just don't include it.
If it was before:
[{'up':[0,1],'down':[0,1],'left':[0,1]}]
to choose the 0th index of the up block and the 1st index of
the down block and drop the left block, the new_gf_struct would
have to be
[{'up':[0],'down':[1]}]
Note that the indices will be renamed to be a 0-based
sequence of integers.
For dropped indices, sumk_to_solver will map to (None,None).
Parameters
----------
new_gf_struct : list of dict
formatted the same as gf_struct_solver:
new_gf_struct[ish][block]=list of indices in that block.
However, the indices are not according to the solver Gf
but the sumk Gf.
"""
gfs = []
# construct gfs, which is the equivalent of new_gf_struct
# but according to the solver Gf, by using the sumk_to_solver
# mapping
for ish in range(len(new_gf_struct)):
gfs.append({})
for block in new_gf_struct[ish].keys():
for ind in new_gf_struct[ish][block]:
ind_sol = self.sumk_to_solver[ish][(block,ind)]
if not ind_sol[0] in gfs[ish]:
gfs[ish][ind_sol[0]]=[]
gfs[ish][ind_sol[0]].append(ind_sol[1])
self.pick_gf_struct_solver(gfs)
def map_gf_struct_solver(self,mapping):
""" Map the Green function structure from one struct to another.
Parameters
----------
mapping : list of dict
the dict consists of elements
(from_block,from_index) : (to_block,to_index)
that maps from one structure to the other
"""
for ish in range(len(mapping)):
gf_struct = {}
so2su = {}
su2so = {}
so2su_block = {}
for frm,to in mapping[ish].iteritems():
if not to[0] in gf_struct:
gf_struct[to[0]]=[]
gf_struct[to[0]].append(to[1])
so2su[to]=self.solver_to_sumk[ish][frm]
su2so[self.solver_to_sumk[ish][frm]]=to
if to[0] in so2su_block:
if so2su_block[to[0]] != \
self.solver_to_sumk_block[ish][frm[0]]:
warn("solver block '{}' maps to more than one sumk block: '{}', '{}'".format(
to[0],so2su_block[to[0]],self.solver_to_sumk_block[ish][frm[0]]))
else:
so2su_block[to[0]]=\
self.solver_to_sumk_block[ish][frm[0]]
for k in self.sumk_to_solver[ish].keys():
if not k in su2so:
su2so[k] = (None,None)
self.gf_struct_solver[ish]=gf_struct
self.solver_to_sumk[ish]=so2su
self.sumk_to_solver[ish]=su2so
self.solver_to_sumk_block[ish]=so2su_block
def create_gf(self,ish=0,gf_function=GfImFreq,**kwargs):
""" Create a zero BlockGf having the gf_struct_solver structure.
When using GfImFreq as gf_function, typically you have to
supply beta as keyword argument.
Parameters
----------
ish : int
shell index
gf_function : constructor
function used to construct the Gf objects constituting the
individual blocks; default: GfImFreq
**kwargs :
options passed on to the Gf constructor for the individual
blocks
"""
names = self.gf_struct_solver[ish].keys()
blocks=[]
for n in names:
G = gf_function(indices=self.gf_struct_solver[ish][n],**kwargs)
blocks.append(G)
G = BlockGf(name_list = names, block_list = blocks)
return G
def convert_gf(self,G,G_struct,ish=0,show_warnings=True,**kwargs):
""" Convert BlockGf from its structure to this structure.
.. warning::
Elements that are zero in the new structure due to
the new block structure will be just ignored, thus
approximated to zero.
Parameters
----------
G : BlockGf
the Gf that should be converted
G_struct : GfStructure
the structure ofthat G
ish : int
shell index
show_warnings : bool
whether to show warnings when elements of the Green's
function get thrown away
**kwargs :
options passed to the constructor for the new Gf
"""
G_new = self.create_gf(ish=ish,**kwargs)
for block in G_struct.gf_struct_solver[ish].keys():
for i1 in G_struct.gf_struct_solver[ish][block]:
for i2 in G_struct.gf_struct_solver[ish][block]:
i1_sumk = G_struct.solver_to_sumk[ish][(block,i1)]
i2_sumk = G_struct.solver_to_sumk[ish][(block,i2)]
i1_sol = self.sumk_to_solver[ish][i1_sumk]
i2_sol = self.sumk_to_solver[ish][i2_sumk]
if i1_sol[0] is None or i2_sol[0] is None:
if show_warnings:
warn(('Element {},{} of block {} of G is not present '+
'in the new structure').format(i1,i2,block))
continue
if i1_sol[0]!=i2_sol[0]:
if show_warnings:
warn(('Element {},{} of block {} of G is approximated '+
'to zero to match the new structure.').format(
i1,i2,block))
continue
G_new[i1_sol[0]][i1_sol[1],i2_sol[1]] = \
G[block][i1,i2]
return G_new
def approximate_as_diagonal(self):
""" Create a structure for a GF with zero off-diagonal elements.
.. warning::
In general, this will throw away non-zero elements of the
Green's function. Be sure to verify whether this approximation
is justified.
"""
self.gf_struct_solver=[]
self.solver_to_sumk=[]
self.solver_to_sumk_block=[]
for ish in range(len(self.sumk_to_solver)):
self.gf_struct_solver.append({})
self.solver_to_sumk.append({})
self.solver_to_sumk_block.append({})
for frm,to in self.sumk_to_solver[ish].iteritems():
if to[0] is not None:
self.gf_struct_solver[ish][frm[0]+'_'+str(frm[1])]=[0]
self.sumk_to_solver[ish][frm]=(frm[0]+'_'+str(frm[1]),0)
self.solver_to_sumk[ish][(frm[0]+'_'+str(frm[1]),0)]=frm
self.solver_to_sumk_block[ish][frm[0]+'_'+str(frm[1])]=frm[0]
def __eq__(self,other):
def compare(one,two):
if type(one)!=type(two):
return False
if one is None and two is None:
return True
if isinstance(one,list) or isinstance(one,tuple):
if len(one) != len(two):
return False
for x,y in zip(one,two):
if not compare(x,y):
return False
return True
elif isinstance(one,int):
return one==two
elif isinstance(one,str):
return one==two
elif isinstance(one,dict):
if set(one.keys()) != set(two.keys()):
return False
for k in set(one.keys()).intersection(two.keys()):
if not compare(one[k],two[k]):
return False
return True
warn('Cannot compare {}'.format(type(one)))
return False
for prop in [ "gf_struct_sumk", "gf_struct_solver",
"solver_to_sumk", "sumk_to_solver", "solver_to_sumk_block"]:
if not compare(getattr(self,prop),getattr(other,prop)):
return False
return True
def copy(self):
return copy.deepcopy(self)
def __reduce_to_dict__(self):
""" Reduce to dict for HDF5 export."""
ret = {}
for element in [ "gf_struct_sumk", "gf_struct_solver",
"solver_to_sumk_block"]:
ret[element] = getattr(self,element)
def construct_mapping(mapping):
d = []
for ish in range(len(mapping)):
d.append({})
for k,v in mapping[ish].iteritems():
d[ish][repr(k)] = repr(v)
return d
ret['solver_to_sumk']=construct_mapping(self.solver_to_sumk)
ret['sumk_to_solver']=construct_mapping(self.sumk_to_solver)
return ret
@classmethod
def __factory_from_dict__(cls,name,D) :
""" Create from dict for HDF5 import."""
def reconstruct_mapping(mapping):
d = []
for ish in range(len(mapping)):
d.append({})
for k,v in mapping[ish].iteritems():
# literal_eval is a saje alternative to eval
d[ish][literal_eval(k)] = literal_eval(v)
return d
D['solver_to_sumk']=reconstruct_mapping(D['solver_to_sumk'])
D['sumk_to_solver']=reconstruct_mapping(D['sumk_to_solver'])
return cls(**D)
def __str__(self):
s=''
s+= "gf_struct_sumk "+str( self.gf_struct_sumk)+'\n'
s+= "gf_struct_solver "+str(self.gf_struct_solver)+'\n'
s+= "solver_to_sumk_block "+str(self.solver_to_sumk_block)+'\n'
for el in ['solver_to_sumk','sumk_to_solver']:
s+=el+'\n'
element=getattr(self,el)
for ish in range(len(element)):
s+=' shell '+str(ish)+'\n'
def keyfun(el):
return '{}_{:05d}'.format(el[0],el[1])
keys = sorted(element[ish].keys(),key=keyfun)
for k in keys:
s+=' '+str(k)+str(element[ish][k])+'\n'
return s
from pytriqs.archive.hdf_archive_schemes import register_class
register_class(BlockStructure)

45
python/sumk_dft.py
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@ -27,12 +27,13 @@ from pytriqs.gf.local import *
import pytriqs.utility.mpi as mpi
from pytriqs.archive import *
from symmetry import *
from block_structure import BlockStructure
from sets import Set
from itertools import product
from warnings import warn
class SumkDFT:
class SumkDFT(object):
"""This class provides a general SumK method for combining ab-initio code and pytriqs."""
def __init__(self, hdf_file, h_field=0.0, use_dft_blocks=False,
@ -53,6 +54,9 @@ class SumkDFT:
use_dft_blocks : boolean, optional
If True, the local Green's function matrix for each spin is divided into smaller blocks
with the block structure determined from the DFT density matrix of the corresponding correlated shell.
Alternatively and additionally, the block structure can be analyzed using :meth:`analyse_block_structure <dft.sumk_dft.SumkDFT.analyse_block_structure>`
and manipulated using the SumkDFT.block_structre attribute (see :class:`BlockStructure <dft.block_structure.BlockStructure>`).
dft_data : string, optional
Name of hdf5 subgroup in which DFT data for projector and lattice Green's function construction are stored.
symmcorr_data : string, optional
@ -112,6 +116,8 @@ class SumkDFT:
self.spin_names_to_ind[iso][
self.spin_block_names[iso][isp]] = isp * self.SP
self.block_structure = BlockStructure()
# GF structure used for the local things in the k sums
# Most general form allowing for all hybridisation, i.e. largest
# blocks possible
@ -221,6 +227,9 @@ class SumkDFT:
if not subgrp in ar:
ar.create_group(subgrp)
for it in things_to_save:
if it in [ "gf_struct_sumk", "gf_struct_solver",
"solver_to_sumk", "sumk_to_solver", "solver_to_sumk_block"]:
warn("It is not recommended to save '{}' individually. Save 'block_structure' instead.".format(it))
try:
ar[subgrp][it] = getattr(self, it)
except:
@ -719,7 +728,7 @@ class SumkDFT:
r"""
Determines the block structure of local Green's functions by analysing the structure of
the corresponding density matrices and the local Hamiltonian. The resulting block structures
for correlated shells are stored in self.gf_struct_solver list.
for correlated shells are stored in the :class:`SumkDFT.block_structure <dft.block_structure.BlockStructure>` attribute.
Parameters
----------
@ -1505,3 +1514,35 @@ class SumkDFT:
atomlst = [shells[i]['atom'] for i in range(len(shells))]
n_atoms = len(set(atomlst))
return n_atoms
# The following methods are here to ensure backward-compatibility
# after introducing the block_structure class
def __get_gf_struct_sumk(self):
return self.block_structure.gf_struct_sumk
def __set_gf_struct_sumk(self,value):
self.block_structure.gf_struct_sumk = value
gf_struct_sumk = property(__get_gf_struct_sumk,__set_gf_struct_sumk)
def __get_gf_struct_solver(self):
return self.block_structure.gf_struct_solver
def __set_gf_struct_solver(self,value):
self.block_structure.gf_struct_solver = value
gf_struct_solver = property(__get_gf_struct_solver,__set_gf_struct_solver)
def __get_solver_to_sumk(self):
return self.block_structure.solver_to_sumk
def __set_solver_to_sumk(self,value):
self.block_structure.solver_to_sumk = value
solver_to_sumk = property(__get_solver_to_sumk,__set_solver_to_sumk)
def __get_sumk_to_solver(self):
return self.block_structure.sumk_to_solver
def __set_sumk_to_solver(self,value):
self.block_structure.sumk_to_solver = value
sumk_to_solver = property(__get_sumk_to_solver,__set_sumk_to_solver)
def __get_solver_to_sumk_block(self):
return self.block_structure.solver_to_sumk_block
def __set_solver_to_sumk_block(self,value):
self.block_structure.solver_to_sumk_block = value
solver_to_sumk_block = property(__get_solver_to_sumk_block,__set_solver_to_sumk_block)

1
test/CMakeLists.txt
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@ -14,3 +14,4 @@ triqs_add_python_test(sumkdft_basic)
triqs_add_python_test(srvo3_Gloc)
triqs_add_python_test(srvo3_transp)
triqs_add_python_test(sigma_from_file)
triqs_add_python_test(blockstructure)

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test/blockstructure.py Normal file
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@ -0,0 +1,83 @@
from pytriqs.applications.dft.sumk_dft import *
from pytriqs.utility.h5diff import h5diff
from pytriqs.gf.local import *
from pytriqs.utility.comparison_tests import assert_block_gfs_are_close
from pytriqs.applications.dft import BlockStructure
SK = SumkDFT('blockstructure.in.h5',use_dft_blocks=True)
original_bs = SK.block_structure
# check pick_gf_struct_solver
pick1 = original_bs.copy()
pick1.pick_gf_struct_solver([{'up_0': [1], 'up_1': [0], 'down_1': [0]}])
# check loading a block_structure from file
SK.block_structure = SK.load(['block_structure'],'mod')[0]
assert SK.block_structure == pick1, 'loading SK block structure from file failed'
# check SumkDFT backward compatibility
sk_pick1 = BlockStructure(gf_struct_sumk = SK.gf_struct_sumk,
gf_struct_solver = SK.gf_struct_solver,
solver_to_sumk = SK.solver_to_sumk,
sumk_to_solver = SK.sumk_to_solver,
solver_to_sumk_block = SK.solver_to_sumk_block)
assert sk_pick1 == pick1, 'constructing block structure from SumkDFT properties failed'
# check pick_gf_struct_sumk
pick2 = original_bs.copy()
pick2.pick_gf_struct_sumk([{'up': [1, 2], 'down': [0,1]}])
# check map_gf_struct_solver
mapping = [{ ('down_0', 0):('down', 0),
('down_0', 1):('down', 2),
('down_1', 0):('down', 1),
('up_0', 0) :('down_1', 0),
('up_0', 1) :('up_0', 0) }]
map1 = original_bs.copy()
map1.map_gf_struct_solver(mapping)
# check create_gf
G1 = original_bs.create_gf(beta=40,n_points=3)
i = 1
for block,gf in G1:
gf << SemiCircular(i)
i+=1
# check approximate_as_diagonal
offd = original_bs.copy()
offd.approximate_as_diagonal()
# check map_gf_struct_solver
G2 = map1.convert_gf(G1,original_bs,beta=40,n_points=3,show_warnings=False)
# check full_structure
full = BlockStructure.full_structure([{'up_0': [0, 1], 'up_1': [0], 'down_1': [0], 'down_0': [0, 1]}],None)
# check __eq__
assert full==full, 'equality not correct (equal structures not equal)'
assert pick1==pick1, 'equality not correct (equal structures not equal)'
assert pick1!=pick2, 'equality not correct (different structures not different)'
assert original_bs!=offd, 'equality not correct (different structures not different)'
if mpi.is_master_node():
with HDFArchive('blockstructure.out.h5','w') as ar:
ar['original_bs'] = original_bs
ar['pick1'] = pick1
ar['pick2'] = pick2
ar['map1'] = map1
ar['offd'] = offd
ar['G1'] = G1
ar['G2'] = G2
ar['full'] = full
# cannot use h5diff because BlockStructure testing is not implemented
# there (and seems difficult to implement because it would mix triqs
# and dft_tools)
with HDFArchive('blockstructure.out.h5','r') as ar,\
HDFArchive('blockstructure.ref.h5','r') as ar2:
for k in ar2:
if isinstance(ar[k],BlockGf):
assert_block_gfs_are_close(ar[k],ar2[k],1.e-6)
else:
assert ar[k]==ar2[k], '{} not equal'.format(k)

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