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[wannier] few minor tidying changes while reading through

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Priyanka Seth 2016-02-23 15:10:22 +01:00
parent 0d3e59a73c
commit 058e8e968f
1 changed files with 168 additions and 146 deletions
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176
python/converters/wannier90_converter.py
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@ -1,5 +1,5 @@
################################################################################
##########################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
@ -18,7 +18,7 @@
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
##########################################################################
###
# Wannier90 to HDF5 converter for the SumkDFT class of dfttools/TRIQS;
@ -49,8 +49,10 @@ import numpy
import math
from pytriqs.archive import *
from converter_tools import *
from itertools import product
import os.path
class Wannier90Converter(ConverterTools):
"""
Conversion from Wannier90 output to an hdf5 file that can be used as input for the SumkDFT class.
@ -77,10 +79,13 @@ class Wannier90Converter(ConverterTools):
"""
self._name = "Wannier90Converter"
assert type(seedname)==StringType, self._name + ": Please provide the DFT files' base name as a string."
if hdf_filename is None: hdf_filename = seedname+'.h5'
assert type(seedname) == StringType, self._name + \
": Please provide the DFT files' base name as a string."
if hdf_filename is None:
hdf_filename = seedname + '.h5'
self.hdf_file = hdf_filename
# if the w90 output is seedname_hr.dat, the input file for the converter must be called seedname.inp
# if the w90 output is seedname_hr.dat, the input file for the
# converter must be called seedname.inp
self.inp_file = seedname + '.inp'
self.w90_seed = seedname
self.dft_subgrp = dft_subgrp
@ -93,7 +98,6 @@ class Wannier90Converter(ConverterTools):
if (os.path.exists(self.hdf_file) and repacking):
ConverterTools.repack(self)
def convert_dft_input(self):
"""
Reads the appropriate files and stores the data for the
@ -106,41 +110,50 @@ class Wannier90Converter(ConverterTools):
"""
# Read and write only on the master node
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
mpi.report("Reading input from %s..." % self.inp_file)
# R is a generator : each R.Next() will return the next number in the file
R = ConverterTools.read_fortran_file(self,self.inp_file,self.fortran_to_replace)
R = ConverterTools.read_fortran_file(
self, self.inp_file, self.fortran_to_replace)
shell_entries = ['atom', 'sort', 'l', 'dim']
corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
# First, let's read the input file with the parameters needed for the conversion
try:
kmesh_mode = int(R.next()) # read k-point mesh generation option
# read k - point mesh generation option
kmesh_mode = int(R.next())
if kmesh_mode >= 0:
# read k-point mesh size from input
nki = [int(R.next()) for idir in range(3)]
else:
# some default grid, if everything else fails...
nki = [8, 8, 8]
density_required = float(R.next()) # read the total number of electrons per cell
# read the total number of electrons per cell
density_required = float(R.next())
# we do not read shells, because we have no additional shells beyond correlated ones,
# and the data will be copied from corr_shells into shells (see below)
n_corr_shells = int(R.next()) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
# number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
n_corr_shells = int(R.next())
# now read the information about the correlated shells (atom, sort, l, dim, SO flag, irep):
corr_shells = [ {name: int(val) for name, val in zip(corr_shell_entries, R)} for icrsh in range(n_corr_shells) ]
corr_shells = [{name: int(val) for name, val in zip(
corr_shell_entries, R)} for icrsh in range(n_corr_shells)]
except StopIteration: # a more explicit error if the file is corrupted.
mpi.report(self._name + ": reading input file %s failed!"%self.inp_file)
mpi.report(self._name + ": reading input file %s failed!" %
self.inp_file)
# close the input file
R.close()
# Set or derive some quantities
symm_op = 0 # Wannier90 does not use symmetries to reduce the k-points
# Wannier90 does not use symmetries to reduce the k-points
# the following might change in future versions
### copy corr_shells into shells (see above)
symm_op = 0
# copy corr_shells into shells (see above)
n_shells = n_corr_shells
shells = []
for ish in range(n_shells):
shells.append({key: corr_shells[ish].get(key,None) for key in shell_entries})
shells.append({key: corr_shells[ish].get(
key, None) for key in shell_entries})
###
SP = 0 # NO spin-polarised calculations for now
SO = 0 # NO spin-orbit calculation for now
@ -150,13 +163,16 @@ class Wannier90Converter(ConverterTools):
# this is more general
n_spin = SP + 1 - SO
dim_corr_shells = sum([sh['dim'] for sh in corr_shells])
mpi.report("Total number of WFs expected in the correlated shells: %d"%dim_corr_shells)
mpi.report(
"Total number of WFs expected in the correlated shells: %d" % dim_corr_shells)
# determine the number of inequivalent correlated shells and maps, needed for further processing
n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(self,corr_shells)
n_inequiv_shells, corr_to_inequiv, inequiv_to_corr = ConverterTools.det_shell_equivalence(
self, corr_shells)
mpi.report("Number of inequivalent shells: %d" % n_inequiv_shells)
mpi.report("Shell representatives: " + format(inequiv_to_corr))
shells_map = [inequiv_to_corr[corr_to_inequiv[ish]] for ish in range(n_corr_shells)]
shells_map = [inequiv_to_corr[corr_to_inequiv[ish]]
for ish in range(n_corr_shells)]
mpi.report("Mapping: " + format(shells_map))
# build the k-point mesh, if its size was given on input (kmesh_mode >= 0),
@ -175,26 +191,26 @@ class Wannier90Converter(ConverterTools):
lmax = ll * (corr_shells[inequiv_to_corr[ish]]['SO'] + 1)
T.append(numpy.zeros([lmax, lmax], numpy.complex_))
spin_w90name = ['_up', '_down']
hamr_full = []
# TODO: generalise to SP=1 (only partially done)
rot_mat_time_inv = [0 for i in range(n_corr_shells)]
# Second, let's read the file containing the Hamiltonian in WF basis produced by Wannier90
for isp in range(n_spin):
### begin loop on isp
# begin loop on isp
# build filename according to wannier90 conventions
if SP == 1:
mpi.report("Reading information for spin component n. %d"%isp)
mpi.report(
"Reading information for spin component n. %d" % isp)
hr_file = self.w90_seed + spin_w90name[isp] + '_hr.dat'
else:
hr_file = self.w90_seed + '_hr.dat'
# now grab the data from the H(R) file
mpi.report("The Hamiltonian in MLWF basis is extracted from %s ..."%hr_file)
mpi.report(
"The Hamiltonian in MLWF basis is extracted from %s ..." % hr_file)
nr, rvec, rdeg, nw, hamr = self.read_wannier90hr(hr_file)
# number of R vectors, their indices, their degeneracy, number of WFs, H(R)
mpi.report("... done: %d R vectors, %d WFs found" % (nr, nw))
@ -230,15 +246,18 @@ class Wannier90Converter(ConverterTools):
mpi.report("Number of WFs equal to number of correlated orbitals")
# we assume spin up and spin down always have same total number of WFs
n_orbitals = numpy.ones([self.n_k,n_spin],numpy.int)*self.nwfs
n_orbitals = numpy.ones(
[self.n_k, n_spin], numpy.int) * self.nwfs
else:
# consistency check between the _up and _down file contents
if nr != self.nrpt: mpi.report("Different number of R vectors for spin-up/spin-down!")
if nw != self.nwfs: mpi.report("Different number of WFs for spin-up/spin-down!")
if nr != self.nrpt:
mpi.report("Different number of R vectors for spin-up/spin-down!")
if nw != self.nwfs:
mpi.report("Different number of WFs for spin-up/spin-down!")
hamr_full.append(hamr)
##FIXME: when do we actually need deepcopy()?
# FIXME: when do we actually need deepcopy()?
# hamr_full.append(deepcopy(hamr))
for ir in range(nr):
@ -265,18 +284,18 @@ class Wannier90Converter(ConverterTools):
for icrsh in range(n_corr_shells):
if not numpy.allclose(rot_mat_[icrsh], rot_mat[icrsh], atol=self._w90zero, rtol=1.e-15):
mpi.report("Rotations for spin component n. %d do not match!" % isp)
### end loop on isp
# end loop on isp
mpi.report("The k-point grid has dimensions: %d, %d, %d" % tuple(nki))
# if calculations are spin-polarized, then renormalize k-point weights
if SP == 1: bz_weights = 0.5 * bz_weights
if SP == 1:
bz_weights = 0.5 * bz_weights
# Third, compute the hoppings in reciprocal space
hopping = numpy.zeros([self.n_k, n_spin, numpy.max(n_orbitals), numpy.max(n_orbitals)], numpy.complex_)
for isp in range(n_spin):
# make Fourier transform H(R) -> H(k) : it can be done one spin at a time
hamk = self.fourierham(self.nwfs, hamr_full[isp])
hamk = self.fourier_ham(self.nwfs, hamr_full[isp])
# copy the H(k) in the right place of hoppings... is there a better way to do this??
for ik in range(self.n_k):
#hopping[ik,isp,:,:] = deepcopy(hamk[ik][:,:])*energy_unit
@ -284,7 +303,8 @@ class Wannier90Converter(ConverterTools):
# Then, initialise the projectors
k_dep_projection = 0 # we always have the same number of WFs at each k-point
proj_mat = numpy.zeros([self.n_k,n_spin,n_corr_shells,max([crsh['dim'] for crsh in corr_shells]),numpy.max(n_orbitals)],numpy.complex_)
proj_mat = numpy.zeros([self.n_k, n_spin, n_corr_shells, max(
[crsh['dim'] for crsh in corr_shells]), numpy.max(n_orbitals)], numpy.complex_)
iorb = 0
# Projectors simply consist in identity matrix blocks selecting those MLWFs that
# correspond to the specific correlated shell indexed by icrsh.
@ -292,22 +312,23 @@ class Wannier90Converter(ConverterTools):
# file and that the ordering of MLWFs matches the corr_shell info from the input.
for icrsh in range(n_corr_shells):
norb = corr_shells[icrsh]['dim']
proj_mat[:,:,icrsh,0:norb,iorb:iorb+norb] = numpy.identity(norb,numpy.complex_)
proj_mat[:, :, icrsh, 0:norb, iorb:iorb +
norb] = numpy.identity(norb, numpy.complex_)
iorb += norb
# Finally, save all required data into the HDF archive:
ar = HDFArchive(self.hdf_file, 'a')
if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp)
if not (self.dft_subgrp in ar):
ar.create_group(self.dft_subgrp)
# The subgroup containing the data. If it does not exist, it is created. If it exists, the data is overwritten!
things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required',
'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat',
'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping',
'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr']
for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it]
for it in things_to_save:
ar[self.dft_subgrp][it] = locals()[it]
del ar
def read_wannier90hr(self, hr_filename="wannier_hr.dat"):
"""
Method for reading the seedname_hr.dat file produced by Wannier90 (http://wannier.org)
@ -333,7 +354,8 @@ class Wannier90Converter(ConverterTools):
"""
# Read only from the master node
if not (mpi.is_master_node()): return
if not (mpi.is_master_node()):
return
try:
with open(hr_filename, "r") as hr_filedesc:
@ -345,7 +367,8 @@ class Wannier90Converter(ConverterTools):
mpi.report("Reading %s..." % hr_filename + hr_data[0])
try:
num_wf = int(hr_data[1]) # reads number of Wannier functions per spin
# reads number of Wannier functions per spin
num_wf = int(hr_data[1])
nrpt = int(hr_data[2])
except ValueError:
mpi.report("Could not read number of WFs or R vectors")
@ -353,7 +376,8 @@ class Wannier90Converter(ConverterTools):
# allocate arrays to save the R vector indexes and degeneracies and the Hamiltonian
rvec_idx = numpy.zeros((nrpt, 3), dtype=int)
rvec_deg = numpy.zeros(nrpt, dtype=int)
h_of_r = [numpy.zeros((num_wf, num_wf), dtype=numpy.complex_) for n in range(nrpt)]
h_of_r = [numpy.zeros((num_wf, num_wf), dtype=numpy.complex_)
for n in range(nrpt)]
# variable currpos points to the current line in the file
currpos = 2
@ -367,25 +391,26 @@ class Wannier90Converter(ConverterTools):
raise IndexError("wrong number of R vectors??")
rvec_deg[ir] = int(x)
ir += 1
# for each direct lattice vector R
for ir in range(nrpt):
# read the block of the Hamiltonian H(R)
for jj in range(num_wf):
for ii in range(num_wf):
# for each direct lattice vector R read the block of the
# Hamiltonian H(R)
for ir, jj, ii in product(range(nrpt), range(num_wf), range(num_wf)):
# advance one line, split the line into tokens
currpos += 1
cline = hr_data[currpos].split()
# check if the orbital indexes in the file make sense
if int(cline[3]) != ii + 1 or int(cline[4]) != jj + 1:
mpi.report("Inconsistent indices at %s%s of R n. %s"%(ii,jj,ir))
rcurr = numpy.array([int(cline[0]), int(cline[1]), int(cline[2])])
mpi.report(
"Inconsistent indices at %s%s of R n. %s" % (ii, jj, ir))
rcurr = numpy.array(
[int(cline[0]), int(cline[1]), int(cline[2])])
if ii == 0 and jj == 0:
rvec_idx[ir] = rcurr
rprec = rcurr
else:
# check if the vector indices are consistent
if not numpy.array_equal(rcurr, rprec):
mpi.report("Inconsistent indices for R vector n. %s"%ir)
mpi.report(
"Inconsistent indices for R vector n. %s" % ir)
# fill h_of_r with the matrix elements of the Hamiltonian
h_of_r[ir][ii, jj] = complex(float(cline[5]), float(cline[6]))
@ -396,8 +421,6 @@ class Wannier90Converter(ConverterTools):
# return the data into variables
return nrpt, rvec_idx, rvec_deg, num_wf, h_of_r
def find_rot_mat(self, n_sh, sh_lst, sh_map, ham0):
"""
Method for finding the matrices that bring from local to global coordinate systems
@ -424,12 +447,14 @@ class Wannier90Converter(ConverterTools):
"""
# initialize the rotation matrices to identities
rot_mat = [numpy.identity(sh_lst[ish]['dim'], dtype=complex) for ish in range(n_sh)]
rot_mat = [numpy.identity(sh_lst[ish]['dim'], dtype=complex)
for ish in range(n_sh)]
istatus = 0
hs = ham0.shape
if hs[0] != hs[1] or hs[0] != sum([sh['dim'] for sh in sh_lst]):
mpi.report("find_rot_mat: wrong block structure of input Hamiltonian!")
mpi.report(
"find_rot_mat: wrong block structure of input Hamiltonian!")
istatus = 0
# this error will lead into troubles later... early return
return istatus, rot_mat
@ -443,7 +468,8 @@ class Wannier90Converter(ConverterTools):
# nw = number of orbitals in this shell
nw = sh_lst[ish]["dim"]
# diagonalize the sub-block of H(0) corresponding to this shell
eigval, eigvec = numpy.linalg.eigh(ham0[iwf:iwf+nw, iwf:iwf+nw])
eigval, eigvec = numpy.linalg.eigh(
ham0[iwf:iwf + nw, iwf:iwf + nw])
# find the indices sorting the eigenvalues in ascending order
eigsrt = eigval[0:nw].argsort()
# order eigenvalues and eigenvectors and save in a list
@ -460,15 +486,20 @@ class Wannier90Converter(ConverterTools):
for ish in range(n_sh):
try:
# build rotation matrices by combining the unitary transformations that diagonalize H(0)
rot_mat[ish] = numpy.dot(eigvec_lst[ish],eigvec_lst[sh_map[ish]].conjugate().transpose())
# build rotation matrices by combining the unitary
# transformations that diagonalize H(0)
rot_mat[ish] = numpy.dot(eigvec_lst[ish], eigvec_lst[
sh_map[ish]].conjugate().transpose())
except ValueError:
mpi.report("Global-to-local rotation matrices cannot be constructed!")
mpi.report(
"Global-to-local rotation matrices cannot be constructed!")
istatus = 1
# check that eigenvalues are the same (within accuracy) for equivalent shells
# check that eigenvalues are the same (within accuracy) for
# equivalent shells
if not numpy.allclose(eigval_lst[ish], eigval_lst[sh_map[ish]], atol=self._w90zero, rtol=1.e-15):
mpi.report("ERROR: eigenvalue mismatch between equivalent shells! %d"%ish)
mpi.report(
"ERROR: eigenvalue mismatch between equivalent shells! %d" % ish)
eigval_diff = eigval_lst[ish] - eigval_lst[sh_map[ish]]
mpi.report("Eigenvalue difference: " + format(eigval_diff))
istatus = 0
@ -477,8 +508,6 @@ class Wannier90Converter(ConverterTools):
return istatus, rot_mat
def kmesh_build(self, msize=None, mmode=0):
"""
Method for the generation of the k-point mesh.
@ -502,27 +531,24 @@ class Wannier90Converter(ConverterTools):
"""
if mmode == 0:
if mmode != 0:
raise ValueError("Mesh generation mode not supported: %s" % mmode)
# a regular mesh including Gamma point
nkpt = msize[0] * msize[1] * msize[2] # total number of k-points
# total number of k-points
nkpt = msize[0] * msize[1] * msize[2]
kmesh = numpy.zeros((nkpt, 3), dtype=float)
ii = 0
for ix in range(msize[0]):
for iy in range(msize[1]):
for iz in range(msize[2]):
for ix, iy, iz in product(range(msize[0]), range(msize[1]), range(msize[2])):
kmesh[ii, :] = [float(ix) / msize[0], float(iy) / msize[1], float(iz) / msize[2]]
ii += 1
# weight is equal for all k-points because wannier90 uses uniform grid on whole BZ
# (normalization is always 1 and takes into account spin degeneracy)
wk = numpy.ones([nkpt], dtype=float) / float(nkpt)
else:
raise ValueError("Mesh generation mode not supported: %s"%mmode)
return nkpt, kmesh, wk
def fourierham(self, norb, h_of_r):
def fourier_ham(self, norb, h_of_r):
"""
Method for obtaining H(k) from H(R) via Fourier transform
The R vectors and k-point mesh are read from global module variables
@ -541,16 +567,12 @@ class Wannier90Converter(ConverterTools):
"""
imag = 1j
twopi = 2 * numpy.pi
h_of_k = [numpy.zeros((norb, norb), dtype=numpy.complex_) for ik in range(self.n_k)]
for ik in range(self.n_k):
ridx = numpy.array(range(self.nrpt))
for ir in ridx:
for ik, ir in product(range(self.n_k), ridx):
rdotk = twopi * numpy.dot(self.k_mesh[ik], self.rvec[ir])
factor = (math.cos(rdotk) + imag * math.sin(rdotk)) / float(self.rdeg[ir])
factor = (math.cos(rdotk) + 1j * math.sin(rdotk)) / float(self.rdeg[ir])
h_of_k[ik][:, :] += factor * h_of_r[ir][:, :]
return h_of_k