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Code Issues Releases Wiki Activity

Updates of Wannier90Converter: (#169)

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Added:

substantial speed-up using MPI for Fourier transform
option to add a local spin-orbit term to t2g local Hamiltonian.
writing dft_fermi_energy to group 'dft_misc_input'
writing kpt_basis to group 'dft_input' if bloch_basis=True
writing kpts_cart to group 'dft_misc_input' if bloch_basis=True
Minor bugfixes:

bug can be caused by rounding of outer window limits if bloch_basis and disentangle =True, made error message clearer
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Sophie Beck 2021-05-06 08:37:15 -04:00 committed by GitHub
parent 0a71b29096
commit 3122ab2a83
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4 changed files with 149 additions and 61 deletions
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202
python/triqs_dft_tools/converters/wannier90.py
View File

@ -25,7 +25,7 @@
#
# written by Gabriele Sclauzero (Materials Theory, ETH Zurich), Dec 2015 -- Jan 2016,
# updated by Maximilian Merkel (Materials Theory, ETH Zurich), Aug 2020 -- Jan 2021,
# and by Sophie Beck (Materials Theory, ETH Zurich), Sep 2020 -- Jan 2021,
# and by Sophie Beck (Materials Theory, ETH Zurich), Sep 2020 -- Apr 2021,
# under the supervision of Claude Ederer (Materials Theory).
# Partially based on previous work by K. Dymkovski and the DFT_tools/TRIQS team.
#
@ -39,8 +39,6 @@
# rot_mat_time_inv also if symm_op = 0?)
# - the calculation of rot_mat in find_rot_mat() relies on the eigenvalues of H(0);
# this might fail in presence of degenerate eigenvalues (now just prints warning)
# - the FFT is always done in serial mode (because all converters run serially);
# this can become very slow with a large number of R-vectors/k-points
# - make the code more MPI safe (error handling): if we run with more than one process
# and an error occurs on the masternode, the calculation does not abort
###
@ -61,7 +59,7 @@ class Wannier90Converter(ConverterTools):
def __init__(self, seedname, hdf_filename=None, dft_subgrp='dft_input',
symmcorr_subgrp='dft_symmcorr_input', misc_subgrp='dft_misc_input',
repacking=False, rot_mat_type='hloc_diag', bloch_basis=False):
repacking=False, rot_mat_type='hloc_diag', bloch_basis=False, add_lambda=None):
"""
Initialise the class.
@ -84,6 +82,8 @@ class Wannier90Converter(ConverterTools):
Can be 'hloc_diag', 'wannier', 'none'
bloch_basis : boolean, optional
Should the Hamiltonian be written in Bloch rather than Wannier basis?
add_lambda : list of floats, optional
add local spin-orbit term
"""
self._name = "Wannier90Converter"
@ -105,6 +105,7 @@ class Wannier90Converter(ConverterTools):
self._w90zero = 2.e-6
self.rot_mat_type = rot_mat_type
self.bloch_basis = bloch_basis
self.add_lambda = add_lambda
if self.rot_mat_type not in ('hloc_diag', 'wannier', 'none'):
raise ValueError('Parameter rot_mat_type invalid, should be one of'
+ '"hloc_diag", "wannier", "none"')
@ -124,9 +125,6 @@ class Wannier90Converter(ConverterTools):
"""
# Read and write only on the master node
if not (mpi.is_master_node()):
return
mpi.report("\nReading input from %s..." % self.inp_file)
# R is a generator : each R.Next() will return the next number in the
@ -184,12 +182,18 @@ class Wannier90Converter(ConverterTools):
if any([corr_shell['SO']==1 for corr_shell in corr_shells]):
SO = 1
SP = 1
print('Spin-orbit interaction turned on')
mpi.report('Spin-orbit interaction turned on')
else:
SO = 0
SP = 0
# Only one block supported - either non-spin-polarized or spin-orbit coupled
assert SP == SO, 'Spin-polarized calculations not implemented'
if self.add_lambda:
assert [sh['dim'] for sh in corr_shells] == [3 for sh in corr_shells], 'Add_lambda only implemented for t2g shell'
assert SO == SP == 0, 'Add_lambda not implemented for SO = SP = 1'
assert self.bloch_basis == False, 'Add_lambda not implemented for bloch_basis = True'
# now setting SO and SP to 1
SO = SP = 1
charge_below = 0 # total charge below energy window NOT used for now
energy_unit = 1.0 # should be understood as eV units
@ -202,6 +206,7 @@ class Wannier90Converter(ConverterTools):
for shell_list in [shells, corr_shells]:
for entry in shell_list:
entry['dim'] *= 2
if 'SO' in entry.keys() and self.add_lambda: entry['SO'] = 1
dim_corr_shells = sum([sh['dim'] for sh in corr_shells])
mpi.report('Total number of WFs expected in the correlated shells: {0:d}'.format(dim_corr_shells))
@ -257,11 +262,33 @@ class Wannier90Converter(ConverterTools):
# now grab the data from the H(R) file
mpi.report(
"\nThe Hamiltonian in MLWF basis is extracted from %s files..." % file_seed)
(nr, rvec, rdeg, nw, hamr, u_mat, udis_mat,
band_mat, k_mesh_from_umat) = self.read_wannier90data(file_seed, kmesh_mode)
# number of R vectors, their indices, their degeneracy, number of
# WFs, H(R)
mpi.report("\n... done: %d R vectors, %d WFs found" % (nr, nw))
nr = rvec = rdeg = nw = hamr = u_mat = udis_mat = band_mat = k_mesh_from_umat = None
if (mpi.is_master_node()):
(nr, rvec, rdeg, nw, hamr, u_mat, udis_mat,
band_mat, k_mesh_from_umat) = self.read_wannier90data(file_seed, kmesh_mode)
mpi.barrier()
nr = mpi.bcast(nr)
rvec = mpi.bcast(rvec)
rdeg = mpi.bcast(rdeg)
nw = mpi.bcast(nw)
hamr = mpi.bcast(hamr)
u_mat = mpi.bcast(u_mat)
udis_mat = mpi.bcast(udis_mat)
band_mat = mpi.bcast(band_mat)
k_mesh_from_umat = mpi.bcast(k_mesh_from_umat)
# number of R vectors, their indices, their degeneracy, number of WFs, H(R),
# U matrices, U(dis) matrices, band energies, k_mesh of U matrices
mpi.report('\n... done: {} R vectors, {} WFs found'.format(nr, nw))
if self.add_lambda:
mpi.report('Adding local spin-orbit term to Hamiltonian (assuming dxz, dyz, dxy as orbital order)')
# upscaling quantities
nw *= 2
hamr = [numpy.kron(numpy.eye(2), hamr[ir]) for ir in range(nr)]
hamr[nr//2] += self.lambda_matrix_w90_t2g()
with numpy.printoptions(linewidth=100, formatter={'complexfloat': '{:+.3f}'.format}):
mpi.report('Local Hamiltonian including spin-orbit coupling:')
mpi.report(hamr[nr//2])
if isp == 0:
# set or check some quantities that must be the same for both
@ -311,7 +338,7 @@ class Wannier90Converter(ConverterTools):
# of WFs
# get second dimension of udis_mat which corresponds to number of bands in window
# n_bands_max corresponds to numpy.max(n_orbitals)
n_bands_max = udis_mat.shape[1]
n_bands_max = udis_mat.shape[1] if not self.add_lambda else 2*udis_mat.shape[1]
n_orbitals = numpy.full([self.n_k, n_spin_blocs], n_bands_max)
else:
# consistency check between the _up and _down file contents
@ -364,19 +391,27 @@ class Wannier90Converter(ConverterTools):
if self.bloch_basis:
if os.path.isfile(self.w90_seed + '.nscf.out'):
fermi_weight_file = self.w90_seed + '.nscf.out'
print('Reading DFT band occupations from Quantum Espresso output {}'.format(fermi_weight_file))
mpi.report('Reading DFT band occupations from Quantum Espresso output {}'.format(fermi_weight_file))
elif os.path.isfile('LOCPROJ'):
assert os.path.isfile('OUTCAR')
fermi_weight_file = 'LOCPROJ'
print('Reading DFT band occupations from Vasp output {}'.format(fermi_weight_file))
mpi.report('Reading DFT band occupations from Vasp output {}'.format(fermi_weight_file))
else:
raise IOError('seedname.nscf.out or LOCPROJ required in bloch_basis mode')
f_weights, band_window, self.fermi_energy = self.convert_misc_input(fermi_weight_file,
self.w90_seed + '.nnkp', n_spin_blocs)
f_weights = band_window = self.fermi_energy = kpt_basis = None
if (mpi.is_master_node()):
f_weights, band_window, self.fermi_energy, kpt_basis = self.convert_misc_input(fermi_weight_file,
self.w90_seed + '.nnkp', n_spin_blocs)
mpi.barrier()
f_weights = mpi.bcast(f_weights)
band_window = mpi.bcast(band_window)
self.fermi_energy = mpi.bcast(self.fermi_energy)
kpt_basis = mpi.bcast(kpt_basis)
# Get density from k-point weighted average and sum over all spins and bands
density_required = numpy.sum(f_weights.T * kpt_weights) * (2 - SP)
print('Overwriting required density with DFT result {:.5f}'.format(density_required))
print('and using the DFT Fermi energy {:.5f} eV\n'.format(self.fermi_energy))
mpi.report('Overwriting required density with DFT result {:.5f}'.format(density_required))
mpi.report('and using the DFT Fermi energy {:.5f} eV\n'.format(self.fermi_energy))
if not self.bloch_basis:
mpi.report("The k-point grid has dimensions: %d, %d, %d" % tuple(nki))
@ -403,7 +438,7 @@ class Wannier90Converter(ConverterTools):
u_temp = numpy.transpose(u_total.conj(),(0,2,1))
for icrsh in range(n_corr_shells):
dim = corr_shells[icrsh]['dim']
proj_mat[:, isp, icrsh, 0:dim, :] = u_temp[:,iorb:iorb+dim,:]
proj_mat[:, isp, icrsh, 0:dim, :] = u_temp[:,iorb:iorb+dim,:] if not self.add_lambda else numpy.kron(numpy.eye(2), u_temp[:,iorb:iorb+dim,:])
iorb += dim
# Then, compute the hoppings in reciprocal space
@ -424,11 +459,11 @@ class Wannier90Converter(ConverterTools):
proj_mat_flattened = proj_mat[ik, isp].reshape(self.nwfs, numpy.max(n_orbitals))
downfolded_ham = proj_mat_flattened.dot(hamk[ik].dot(proj_mat_flattened.conj().T))
if not numpy.allclose(downfolded_ham, wannier_ham[ik], atol=self._w90zero, rtol=0):
if not numpy.allclose(downfolded_ham, wannier_ham[ik], atol=1e-4, rtol=0):
mpi.report('WARNING: mismatch between downfolded Hamiltonian and '
+ f'Fourier transformed H(R). First occurred at kpt {ik}:')
with numpy.printoptions(formatter={'complexfloat': '{:+.3f}'.format}):
with numpy.printoptions(formatter={'complexfloat': '{:+.4f}'.format}):
mpi.report('Downfolded Hamiltonian, P H_eig P')
mpi.report(downfolded_ham)
mpi.report('\nWannier Hamiltonian, Fourier(H(r))')
@ -450,24 +485,29 @@ class Wannier90Converter(ConverterTools):
# Finally, save all required data into the HDF archive:
# use_rotations is supposed to be an int = 0, 1, no bool
use_rotations = int(use_rotations)
with HDFArchive(self.hdf_file, 'a') as ar:
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', 'kpt_weights', 'kpts']
for it in things_to_save:
ar[self.dft_subgrp][it] = locals()[it]
if mpi.is_master_node():
with HDFArchive(self.hdf_file, 'a') as ar:
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', 'kpt_weights', 'kpts']
if self.bloch_basis: numpy.append(things_to_save, 'kpt_basis')
for it in things_to_save:
ar[self.dft_subgrp][it] = locals()[it]
if self.bloch_basis:
# Store Fermi weights to 'dft_misc_input'
if not (self.misc_subgrp in ar):
ar.create_group(self.misc_subgrp)
ar[self.misc_subgrp]['dft_fermi_weights'] = f_weights
ar[self.misc_subgrp]['band_window'] = band_window+1 # Change to 1-based index
ar[self.misc_subgrp]['dft_fermi_energy'] = self.fermi_energy
if self.bloch_basis:
ar[self.misc_subgrp]['dft_fermi_weights'] = f_weights
ar[self.misc_subgrp]['band_window'] = band_window+1 # Change to 1-based index
ar[self.misc_subgrp]['kpts_cart'] = numpy.dot(kpts, kpt_basis.T)
mpi.barrier()
def read_wannier90data(self, wannier_seed="wannier", kmesh_mode=0):
"""
@ -502,10 +542,6 @@ class Wannier90Converter(ConverterTools):
If not self.bloch_basis unused and therefore None
"""
# Read only from the master node
if not (mpi.is_master_node()):
return
hr_filename = wannier_seed + '_hr.dat'
try:
with open(hr_filename, 'r') as hr_filedesc:
@ -675,7 +711,10 @@ class Wannier90Converter(ConverterTools):
udis_mat = numpy.zeros([n_k, num_ks_bands, num_wf], dtype=complex)
for ik in range(n_k):
udis_mat[ik, inside_window[ik]] = udis_data[ik, :, :n_inside_per_k[ik]].T
assert numpy.allclose(udis_data[ik, :, n_inside_per_k[ik]:], 0)
if not numpy.allclose(udis_data[ik, :, n_inside_per_k[ik]:], 0):
raise ValueError('This error could come from rounding of the band window in the seedname.wout. '
+ 'Never use default outer window but something wider and '
+ 'check that your outer window is not close to any band energy.')
else:
# no disentanglement; fill udis_mat with identity
udis_mat = numpy.array([numpy.identity(num_wf,dtype=complex)] * n_k)
@ -861,11 +900,18 @@ class Wannier90Converter(ConverterTools):
h_of_k = [numpy.zeros((self.nwfs, self.nwfs), dtype=complex)
for ik in range(self.n_k)]
h_of_k_array = numpy.array(h_of_k, dtype=complex)
ridx = numpy.array(list(range(self.nrpt)))
for ik, ir in product(list(range(self.n_k)), ridx):
rdotk = numpy.dot(self.kpts[ik], self.rvec[ir])
factor = numpy.exp(2j * numpy.pi * rdotk) / self.rdeg[ir]
h_of_k[ik][:, :] += factor * h_of_r[ir][:, :]
for ir in mpi.slice_array(ridx):
for ik in list(range(self.n_k)):
rdotk = numpy.dot(self.kpts[ik], self.rvec[ir])
factor = numpy.exp(2j * numpy.pi * rdotk) / self.rdeg[ir]
h_of_k_array[ik, :, :] += factor * h_of_r[ir][:, :]
h_of_k_array = mpi.all_reduce(mpi.world, h_of_k_array, lambda x, y: x + y)
mpi.barrier()
h_of_k = list(h_of_k_array[:])
return h_of_k
@ -890,30 +936,34 @@ class Wannier90Converter(ConverterTools):
band indices of correlated subspace
fermi_energy : float
the DFT Kohn-Sham Fermi energy
kpt_basis: numpy.array[3, 3]
the basis vectors in reciprocal space
"""
# Read only from the master node
if not (mpi.is_master_node()):
return
assert n_spin_blocs == 1, 'spin-polarized not implemented'
assert 'nscf.out' in out_filename or out_filename == 'LOCPROJ'
occupations = []
reading_kpt_basis = False
lines_read_kpt_basis = 0
kpt_basis = numpy.zeros((3, 3))
if 'nscf.out' in out_filename:
occupations = []
with open(out_filename,'r') as out_file:
out_data = out_file.readlines()
# Reads number of Kohn-Sham states and total number of electrons
# Reads number of Kohn-Sham states and Fermi energy
for line in out_data:
if 'number of electrons' in line:
n_total_electrons = float(line.split()[-1])
if 'number of Kohn-Sham states' in line:
n_ks = int(line.split()[-1])
if 'Fermi energy' in line:
elif 'Fermi energy' in line:
fermi_energy = float(line.split()[-2])
elif 'reciprocal axes' in line:
reading_kpt_basis = True
continue
elif reading_kpt_basis and lines_read_kpt_basis < 3:
kpt_basis[lines_read_kpt_basis, :] = line.split()[3:6]
lines_read_kpt_basis +=1
# get occupations
for ct, line in enumerate(out_data):
@ -943,6 +993,17 @@ class Wannier90Converter(ConverterTools):
occupations = numpy.loadtxt((line for line in file if 'orbital' in line), usecols=5)
occupations = occupations.reshape((self.n_k, n_ks))
# Read reciprocal vectors from OUTCAR
with open('OUTCAR', 'r') as file:
for line in file:
if 'reciprocal lattice vectors' in line:
reading_kpt_basis = True
elif reading_kpt_basis:
kpt_basis[lines_read_kpt_basis, :] = line.split()[3:6]
lines_read_kpt_basis += 1
if lines_read_kpt_basis == 3:
break
# assume that all bands contribute, then remove from exclude_bands; python indexing
corr_bands = list(range(n_ks))
# read exclude_bands from "seedname.nnkp" file
@ -977,4 +1038,31 @@ class Wannier90Converter(ConverterTools):
f_weights = included_occupations.reshape(included_occupations.shape[0], 1,
included_occupations.shape[1])
return f_weights, band_window, fermi_energy
return f_weights, band_window, fermi_energy, kpt_basis
def lambda_matrix_w90_t2g(self):
"""
Adds local spin-orbit interaction term to the t2g subspace. Orbital order is assumed to be
xz_up, yz_up, xy_up, xz_dn, yz_dn, xy_dn as given by Wannier90 per default.
Parameters are defined as self.add_lambda = [lambda_x, lambda_y, lambda_z], representative of
the orbital coupling terms perpendicular to [x, y, z] i.e. [d_yz, d_xz, d_xy], respectively.
Returns
-------
lambda_matrix : numpy.array[6, 6]
local spin-orbit term to be added to H(0)
"""
lambda_x, lambda_y, lambda_z = self.add_lambda
lambda_matrix = numpy.zeros((6,6), dtype=complex)
lambda_matrix[0,1] = -1j*lambda_z/2.0
lambda_matrix[0,5] = 1j*lambda_x/2.0
lambda_matrix[1,5] = -lambda_y/2.0
lambda_matrix[2,3] = -1j*lambda_x/2.0
lambda_matrix[2,4] = lambda_y/2.0
lambda_matrix[3,4] = 1j*lambda_z/2.0
lambda_matrix += numpy.transpose(numpy.conjugate(lambda_matrix))
return lambda_matrix

8
test/python/w90_convert.py
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@ -27,17 +27,17 @@ from triqs.utility.h5diff import h5diff
import triqs.utility.mpi as mpi
# test rot_mat_type='hloc_diag'
Converter = Wannier90Converter(seedname='LaVO3-Pbnm',hdf_filename='w90_convert.out.h5', rot_mat_type='hloc_diag')
Converter = Wannier90Converter(seedname='LaVO3-Pbnm',hdf_filename='w90_convert_hloc_diag.out.h5', rot_mat_type='hloc_diag')
Converter.convert_dft_input()
if mpi.is_master_node():
h5diff("w90_convert.out.h5","w90_convert_hloc_diag.ref.h5")
h5diff("w90_convert_hloc_diag.out.h5","w90_convert_hloc_diag.ref.h5")
# test rot_mat_type='wannier'
Converter = Wannier90Converter(seedname='LaVO3-Pnma',hdf_filename='w90_convert.out.h5', rot_mat_type='wannier')
Converter = Wannier90Converter(seedname='LaVO3-Pnma',hdf_filename='w90_convert_wannier.out.h5', rot_mat_type='wannier')
Converter.convert_dft_input()
if mpi.is_master_node():
h5diff("w90_convert.out.h5","w90_convert_wannier.ref.h5")
h5diff("w90_convert_wannier.out.h5","w90_convert_wannier.ref.h5")

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test/python/w90_convert_hloc_diag.ref.h5
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test/python/w90_convert_wannier.ref.h5
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