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read wannier centres and symmetry kpath from w90 (#253)

Browse Source 
This PR/ commit adds two new features to the w90 converter stored to the h5 archive: 
1. Centres of Wannier functions: This can be obtained using the `read_wannier90_centres()` function. This would also be useful if one wants to shift Wannier centres back to the home unit cells on-the-fly in `dft_tool`. 
2. High-symmetry k-path for band structure: This can be obtained using the `read_wannier90_symm_kpath()` function. 

changes:
* read wannier centres and symmetry kpath from w90
* [fix] w90convert test after fix for kpt_basis stor

---------

Co-authored-by: Alexander Hampel <ahampel@flatironinstitute.org>
This commit is contained in:
Chia-Nan Yeh 2024-06-03 15:00:01 -04:00 committed by GitHub
parent a87276b6c4
commit b8a667b3a1
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5 changed files with 430 additions and 5 deletions
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86
python/triqs_dft_tools/converters/wannier90.py
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@ -166,8 +166,15 @@ class Wannier90Converter(ConverterTools):
# Second, let's read the file containing the Hamiltonian in WF basis # Second, let's read the file containing the Hamiltonian in WF basis
# produced by Wannier90 # produced by Wannier90
(wannier_hr, u_total, ks_eigenvals, r_vector, r_degeneracy, n_wannier, n_bands, (wannier_hr, u_total, ks_eigenvals, r_vector, r_degeneracy, n_wannier, n_bands,
k_mesh_from_umat) = read_all_wannier90_data(n_spin_blocks, dim_corr_shells, self.w90_seed, k_mesh_from_umat, wan_centres) = read_all_wannier90_data(n_spin_blocks, dim_corr_shells,
self.add_lambda, self.bloch_basis) self.w90_seed, self.add_lambda,
self.bloch_basis)
# Read high-symmetry k-path from _band.kpt
w90_kpath_results = None
if mpi.is_master_node():
w90_kpath_results = read_wannier90_symm_kpath(self.w90_seed)
symm_kpath_info = mpi.bcast(w90_kpath_results)
# Builds kmesh or uses kmesh from _u.mat # Builds kmesh or uses kmesh from _u.mat
if self.bloch_basis: if self.bloch_basis:
@ -315,8 +322,10 @@ class Wannier90Converter(ConverterTools):
'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat', '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', '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', 'dft_code'] 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'kpt_weights', 'kpts', 'dft_code']
if wan_centres is not None:
things_to_save.append('wan_centres')
if self.bloch_basis: if self.bloch_basis:
np.append(things_to_save, 'kpt_basis') things_to_save.append('kpt_basis')
for it in things_to_save: for it in things_to_save:
archive[self.dft_subgrp][it] = locals()[it] archive[self.dft_subgrp][it] = locals()[it]
@ -324,6 +333,12 @@ class Wannier90Converter(ConverterTools):
if self.misc_subgrp not in archive: if self.misc_subgrp not in archive:
archive.create_group(self.misc_subgrp) archive.create_group(self.misc_subgrp)
archive[self.misc_subgrp]['dft_fermi_energy'] = fermi_energy archive[self.misc_subgrp]['dft_fermi_energy'] = fermi_energy
if symm_kpath_info is not None:
archive[self.misc_subgrp].create_group('symm_kpath')
kpath_grp = archive[self.misc_subgrp]['symm_kpath']
kpath_grp['kpts'] = symm_kpath_info[0]
kpath_grp['labels'] = symm_kpath_info[1]
kpath_grp['label_idx'] = symm_kpath_info[2]
if self.bloch_basis: if self.bloch_basis:
archive[self.misc_subgrp]['dft_fermi_weights'] = f_weights archive[self.misc_subgrp]['dft_fermi_weights'] = f_weights
archive[self.misc_subgrp]['band_window'] = band_window+1 # Change to 1-based index archive[self.misc_subgrp]['band_window'] = band_window+1 # Change to 1-based index
@ -665,6 +680,59 @@ def read_wannier90_blochbasis_data(wannier_seed, n_wannier_spin):
return u_mat_spin, udis_mat_spin, ks_eigenvals_spin, k_mesh return u_mat_spin, udis_mat_spin, ks_eigenvals_spin, k_mesh
def read_wannier90_centres(wannier_seed):
centres_filename = wannier_seed + '_centres.xyz'
if not os.path.isfile(centres_filename):
mpi.report(f'Wannier centres file, {centres_filename}, does not exist. Please set: '
'write_xyz = true, translate_home_cell = false if you want to use the centres.')
return None
else:
mpi.report(f'Wannier centres read from file: {centres_filename}')
centres = []
with open(centres_filename, 'r') as c_file:
c_data = c_file.readlines()
mpi.report('Reading {}: {}'.format(centres_filename, c_data[1].strip()))
for l in c_data:
if l[0] == 'X':
x = np.asarray(l.split())
R = x[1:].astype(float)
centres.append(R)
centres = np.asarray(centres)
return centres
def read_wannier90_symm_kpath(wannier_seed):
kpath_filename = wannier_seed + '_band.kpt'
label_filename = wannier_seed + '_band.labelinfo.dat'
if not os.path.isfile(kpath_filename) or not os.path.isfile(label_filename):
return None
labels = ''
label_idx = []
with open(label_filename, 'r') as label_file:
label_data = label_file.readlines()
for line in label_data:
l, idx = line.split()[:2]
labels += l
label_idx.append(int(idx))
label_idx = np.asarray(label_idx)
kpts_interpolate = []
with open(kpath_filename, 'r') as path_file:
linelist = path_file.readlines()
mpi.report('Reading {}: high-symmetry path \'{}\' for '
'band structure'.format(kpath_filename, labels))
for line in linelist[1:]:
x = np.asarray(line.split()[:-1])
x = x.astype(float)
kpts_interpolate.append(x)
kpts_interpolate = np.asarray(kpts_interpolate)
return kpts_interpolate, labels, label_idx
def read_all_wannier90_data(n_spin_blocks, dim_corr_shells, w90_seed, add_lambda, bloch_basis): def read_all_wannier90_data(n_spin_blocks, dim_corr_shells, w90_seed, add_lambda, bloch_basis):
""" """
Reads in all the wannier90 data using the functions read_wannier90_hr_data Reads in all the wannier90 data using the functions read_wannier90_hr_data
@ -690,9 +758,12 @@ def read_all_wannier90_data(n_spin_blocks, dim_corr_shells, w90_seed, add_lambda
Number of bands Number of bands
k_mesh_from_umat : np.ndarray[n_k, 3] of float k_mesh_from_umat : np.ndarray[n_k, 3] of float
The k points as used in wannier for consistency. None if not bloch_basis The k points as used in wannier for consistency. None if not bloch_basis
centres: np.ndarray[n_spin_blocks, 3, 3] of float or None
Centres of wannier functions
""" """
spin_w90name = ['_up', '_down'] spin_w90name = ['_up', '_down']
wannier_hr = [] wannier_hr = []
centres = []
if bloch_basis: if bloch_basis:
u_mat = [] u_mat = []
udis_mat = [] udis_mat = []
@ -721,6 +792,11 @@ def read_all_wannier90_data(n_spin_blocks, dim_corr_shells, w90_seed, add_lambda
# U matrices, U(dis) matrices, band energies, k_mesh of U matrices # U matrices, U(dis) matrices, band energies, k_mesh of U matrices
u_mat_spin, udis_mat_spin, ks_eigenvals_spin, k_mesh_from_umat = mpi.bcast(w90_results) u_mat_spin, udis_mat_spin, ks_eigenvals_spin, k_mesh_from_umat = mpi.bcast(w90_results)
w90_centres_results = None
if mpi.is_master_node():
w90_centres_results = read_wannier90_centres(file_seed)
centres_spin = mpi.bcast(w90_centres_results)
mpi.report('\n... done: {} R vectors, {} WFs found'.format(n_r_spin, n_wannier_spin)) mpi.report('\n... done: {} R vectors, {} WFs found'.format(n_r_spin, n_wannier_spin))
if add_lambda: if add_lambda:
@ -763,6 +839,7 @@ def read_all_wannier90_data(n_spin_blocks, dim_corr_shells, w90_seed, add_lambda
assert np.all(r_degeneracy_spin == r_degeneracy), 'R vec. degeneracy different between spin components' assert np.all(r_degeneracy_spin == r_degeneracy), 'R vec. degeneracy different between spin components'
wannier_hr.append(wannier_hr_spin) wannier_hr.append(wannier_hr_spin)
centres.append(centres_spin)
if bloch_basis: if bloch_basis:
u_mat.append(u_mat_spin) u_mat.append(u_mat_spin)
udis_mat.append(udis_mat_spin) udis_mat.append(udis_mat_spin)
@ -777,9 +854,10 @@ def read_all_wannier90_data(n_spin_blocks, dim_corr_shells, w90_seed, add_lambda
ks_eigenvals = None ks_eigenvals = None
k_mesh_from_umat = None k_mesh_from_umat = None
wannier_hr = np.array(wannier_hr) wannier_hr = np.array(wannier_hr)
centres = np.array(centres) if centres[0] is not None else None
return (wannier_hr, u_total, ks_eigenvals, r_vector, r_degeneracy, return (wannier_hr, u_total, ks_eigenvals, r_vector, r_degeneracy,
n_wannier, n_bands, k_mesh_from_umat) n_wannier, n_bands, k_mesh_from_umat, centres)
def build_kmesh(kmesh_size, kmesh_mode=0): def build_kmesh(kmesh_size, kmesh_mode=0):

343
test/python/w90_convert/SrVO3_col_band.kpt Normal file
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4
test/python/w90_convert/SrVO3_col_band.labelinfo.dat Normal file
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test/python/w90_convert/SrVO3_col_blochbasis.ref.h5
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test/python/w90_convert/SrVO3_col_wannierbasis.ref.h5
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