mirror of
https://github.com/triqs/dft_tools
synced 2024-11-18 12:03:50 +01:00
f27399758e
merged unstable into py3
* include the major changes of a94f8ed942
of blockstructure.py
* adapted all code to python 3
* fixed all tests
507 lines
20 KiB
Python
507 lines
20 KiB
Python
|
|
################################################################################
|
|
#
|
|
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
|
|
#
|
|
# Copyright (C) 2011 by M. Ferrero, O. Parcollet
|
|
#
|
|
# DFT tools: Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
|
|
#
|
|
# PLOVasp: Copyright (C) 2015 by O. E. Peil
|
|
#
|
|
# TRIQS is free software: you can redistribute it and/or modify it under the
|
|
# terms of the GNU General Public License as published by the Free Software
|
|
# Foundation, either version 3 of the License, or (at your option) any later
|
|
# version.
|
|
#
|
|
# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
|
|
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
|
|
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
|
|
# details.
|
|
#
|
|
# You should have received a copy of the GNU General Public License along with
|
|
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
|
#
|
|
################################################################################
|
|
r"""
|
|
plovasp.proj_shell
|
|
==================
|
|
|
|
Storage and manipulation on projector shells.
|
|
"""
|
|
def issue_warning(message):
|
|
"""
|
|
Issues a warning.
|
|
"""
|
|
print()
|
|
print(" !!! WARNING !!!: " + message)
|
|
print()
|
|
|
|
import itertools as it
|
|
import numpy as np
|
|
from . import atm
|
|
|
|
np.set_printoptions(suppress=True)
|
|
|
|
################################################################################
|
|
################################################################################
|
|
#
|
|
# class ProjectorShell
|
|
#
|
|
################################################################################
|
|
################################################################################
|
|
class ProjectorShell:
|
|
"""
|
|
Container of projectors related to a specific shell.
|
|
|
|
The constructor pre-selects a subset of projectors according to
|
|
the shell parameters passed from the config-file.
|
|
|
|
Parameters:
|
|
|
|
- sh_pars (dict) : shell parameters from the config-file
|
|
- proj_raw (numpy.array) : array of raw projectors
|
|
|
|
"""
|
|
def __init__(self, sh_pars, proj_raw, proj_params, kmesh, structure, nc_flag):
|
|
self.lorb = sh_pars['lshell']
|
|
self.ions = sh_pars['ions']
|
|
self.user_index = sh_pars['user_index']
|
|
self.corr = sh_pars['corr']
|
|
self.ion_sort = [sh_pars['ion_sort']]
|
|
self.nc_flag = nc_flag
|
|
# try:
|
|
# self.tmatrix = sh_pars['tmatrix']
|
|
# except KeyError:
|
|
# self.tmatrix = None
|
|
|
|
self.lm1 = self.lorb**2
|
|
self.lm2 = (self.lorb+1)**2
|
|
|
|
self.nion = self.ions['nion']
|
|
# Extract ion list and equivalence classes (ion sorts)
|
|
self.ion_list = sorted(it.chain(*self.ions['ion_list']))
|
|
|
|
if self.ion_sort[0] is None:
|
|
self.ion_sort = []
|
|
for ion in self.ion_list:
|
|
for icl, eq_cl in enumerate(self.ions['ion_list']):
|
|
if ion in eq_cl:
|
|
self.ion_sort.append(icl + 1) # Enumerate classes starting from 1
|
|
break
|
|
|
|
self.ndim = self.extract_tmatrices(sh_pars)
|
|
|
|
self.extract_projectors(proj_raw, proj_params, kmesh, structure)
|
|
|
|
################################################################################
|
|
#
|
|
# extract_tmatrices
|
|
#
|
|
################################################################################
|
|
def extract_tmatrices(self, sh_pars):
|
|
"""
|
|
Extracts and interprets transformation matrices provided by the
|
|
config-parser.
|
|
There are two relevant options in 'sh_pars':
|
|
|
|
'tmatrix' : a transformation matrix applied to all ions in the shell
|
|
'tmatrices': interpreted as a set of transformation matrices for each ion.
|
|
|
|
If both of the options are present a warning is issued and 'tmatrices'
|
|
supersedes 'tmatrix'.
|
|
|
|
Flag 'self.do_transform' is introduced for the optimization purposes
|
|
to avoid superfluous matrix multiplications.
|
|
"""
|
|
nion = self.nion
|
|
nm = self.lm2 - self.lm1
|
|
|
|
if 'tmatrices' in sh_pars:
|
|
self.do_transform = True
|
|
|
|
if 'tmatrix' in sh_pars:
|
|
mess = "Both TRANSFORM and TRANSFILE are specified, TRANSFORM will be ignored."
|
|
issue_warning(mess)
|
|
|
|
raw_matrices = sh_pars['tmatrices']
|
|
nrow, ncol = raw_matrices.shape
|
|
|
|
assert nrow%nion == 0, "Number of rows in TRANSFILE must be divisible by the number of ions"
|
|
assert ncol%nm == 0, "Number of columns in TRANSFILE must be divisible by the number of orbitals 2*l + 1"
|
|
|
|
nr = nrow // nion
|
|
nsize = ncol // nm
|
|
assert nsize in (1, 2, 4), "Number of columns in TRANSFILE must be divisible by either 1, 2, or 4"
|
|
#
|
|
# Determine the spin-dimension and whether the matrices are real or complex
|
|
#
|
|
# if nsize == 1 or nsize == 2:
|
|
# Matrices (either real or complex) are spin-independent
|
|
# nls_dim = nm
|
|
# if msize == 2:
|
|
# is_complex = True
|
|
# else:
|
|
# is_complex = False
|
|
# elif nsize = 4:
|
|
# Matrices are complex and spin-dependent
|
|
# nls_dim = 2 * nm
|
|
# is_complex = True
|
|
#
|
|
is_complex = nsize > 1
|
|
ns_dim = max(1, nsize // 2)
|
|
|
|
# Dimension of the orbital subspace
|
|
assert nr%ns_dim == 0, "Number of rows in TRANSFILE is not compatible with the spin dimension"
|
|
ndim = nr // ns_dim
|
|
|
|
self.tmatrices = np.zeros((nion, nr, nm * ns_dim), dtype=np.complex128)
|
|
|
|
if is_complex:
|
|
raw_matrices = raw_matrices[:, ::2] + raw_matrices[:, 1::2] * 1j
|
|
|
|
for io in range(nion):
|
|
i1 = io * nr
|
|
i2 = (io + 1) * nr
|
|
self.tmatrices[io, :, :] = raw_matrices[i1:i2, :]
|
|
|
|
return ndim
|
|
|
|
if 'tmatrix' in sh_pars:
|
|
self.do_transform = True
|
|
|
|
raw_matrix = sh_pars['tmatrix']
|
|
nrow, ncol = raw_matrix.shape
|
|
|
|
assert ncol%nm == 0, "Number of columns in TRANSFORM must be divisible by the number of orbitals 2*l + 1"
|
|
|
|
# Only spin-independent matrices are expected here
|
|
nsize = ncol // nm
|
|
assert nsize in (1, 2), "Number of columns in TRANSFORM must be divisible by either 1 or 2"
|
|
|
|
is_complex = nsize > 1
|
|
if is_complex:
|
|
matrix = raw_matrix[:, ::2] + raw_matrix[:, 1::2] * 1j
|
|
else:
|
|
matrix = raw_matrix
|
|
|
|
ndim = nrow
|
|
|
|
self.tmatrices = np.zeros((nion, nrow, nm), dtype=np.complex128)
|
|
for io in range(nion):
|
|
self.tmatrices[io, :, :] = raw_matrix
|
|
|
|
return ndim
|
|
|
|
# If no transformation matrices are provided define a default one
|
|
self.do_transform = False
|
|
|
|
ns_dim = 2 if self.nc_flag else 1
|
|
ndim = nm * ns_dim
|
|
|
|
# We still need the matrices for the output
|
|
self.tmatrices = np.zeros((nion, ndim, ndim), dtype=np.complex128)
|
|
for io in range(nion):
|
|
self.tmatrices[io, :, :] = np.identity(ndim, dtype=np.complex128)
|
|
|
|
return ndim
|
|
|
|
################################################################################
|
|
#
|
|
# extract_projectors
|
|
#
|
|
################################################################################
|
|
def extract_projectors(self, proj_raw, proj_params, kmesh, structure):
|
|
"""
|
|
Extracts projectors for the given shell.
|
|
|
|
Projectors are selected from the raw-projector array 'proj_raw'
|
|
according to the shell parameters.
|
|
If necessary the projectors are transformed usin 'self.tmatrices'.
|
|
"""
|
|
assert self.nc_flag == False, "Non-collinear case is not implemented"
|
|
|
|
# nion = len(self.ion_list)
|
|
nion = self.nion
|
|
nlm = self.lm2 - self.lm1
|
|
_, ns, nk, nb = proj_raw.shape
|
|
|
|
if self.do_transform:
|
|
# TODO: implement a non-collinear case
|
|
# for a non-collinear case 'ndim' is 'ns * nm'
|
|
ndim = self.tmatrices.shape[1]
|
|
self.proj_arr = np.zeros((nion, ns, nk, ndim, nb), dtype=np.complex128)
|
|
for ik in range(nk):
|
|
kp = kmesh['kpoints'][ik]
|
|
for io, ion in enumerate(self.ion_list):
|
|
proj_k = np.zeros((ns, nlm, nb), dtype=np.complex128)
|
|
qcoord = structure['qcoords'][ion]
|
|
# kphase = np.exp(-2.0j * np.pi * np.dot(kp, qcoord))
|
|
# kphase = 1.0
|
|
for m in range(nlm):
|
|
# Here we search for the index of the projector with the given isite/l/m indices
|
|
for ip, par in enumerate(proj_params):
|
|
if par['isite'] - 1 == ion and par['l'] == self.lorb and par['m'] == m:
|
|
proj_k[:, m, :] = proj_raw[ip, :, ik, :] #* kphase
|
|
break
|
|
for isp in range(ns):
|
|
self.proj_arr[io, isp, ik, :, :] = np.dot(self.tmatrices[io, :, :], proj_k[isp, :, :])
|
|
|
|
else:
|
|
# No transformation: just copy the projectors as they are
|
|
self.proj_arr = np.zeros((nion, ns, nk, nlm, nb), dtype=np.complex128)
|
|
for io, ion in enumerate(self.ion_list):
|
|
qcoord = structure['qcoords'][ion]
|
|
for m in range(nlm):
|
|
# Here we search for the index of the projector with the given isite/l/m indices
|
|
for ip, par in enumerate(proj_params):
|
|
if par['isite'] - 1 == ion and par['l'] == self.lorb and par['m'] == m:
|
|
self.proj_arr[io, :, :, m, :] = proj_raw[ip, :, :, :]
|
|
# for ik in range(nk):
|
|
# kp = kmesh['kpoints'][ik]
|
|
## kphase = np.exp(-2.0j * np.pi * np.dot(kp, qcoord))
|
|
# kphase = 1.0
|
|
# self.proj_arr[io, :, :, m, :] = proj_raw[ip, :, :, :] # * kphase
|
|
break
|
|
|
|
|
|
################################################################################
|
|
#
|
|
# select_projectors
|
|
#
|
|
################################################################################
|
|
def select_projectors(self, ib_win, ib_min, ib_max):
|
|
"""
|
|
Selects a subset of projectors corresponding to a given energy window.
|
|
"""
|
|
self.ib_win = ib_win
|
|
self.ib_min = ib_min
|
|
self.ib_max = ib_max
|
|
nb_max = ib_max - ib_min + 1
|
|
|
|
# Set the dimensions of the array
|
|
nion, ns, nk, nlm, nbtot = self.proj_arr.shape
|
|
# !!! Note that the order of the two last indices is different !!!
|
|
self.proj_win = np.zeros((nion, ns, nk, nlm, nb_max), dtype=np.complex128)
|
|
|
|
# Select projectors for a given energy window
|
|
ns_band = self.ib_win.shape[1]
|
|
for isp in range(ns):
|
|
for ik in range(nk):
|
|
# TODO: for non-collinear case something else should be done here
|
|
is_b = min(isp, ns_band)
|
|
ib1 = self.ib_win[ik, is_b, 0]
|
|
ib2 = self.ib_win[ik, is_b, 1] + 1
|
|
ib_win = ib2 - ib1
|
|
self.proj_win[:, isp, ik, :, :ib_win] = self.proj_arr[:, isp, ik, :, ib1:ib2]
|
|
|
|
################################################################################
|
|
#
|
|
# density_matrix
|
|
#
|
|
################################################################################
|
|
def density_matrix(self, el_struct, site_diag=True, spin_diag=True):
|
|
"""
|
|
Returns occupation matrix/matrices for the shell.
|
|
"""
|
|
nion, ns, nk, nlm, nbtot = self.proj_win.shape
|
|
|
|
# assert site_diag, "site_diag = False is not implemented"
|
|
assert spin_diag, "spin_diag = False is not implemented"
|
|
|
|
if site_diag:
|
|
occ_mats = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
|
|
overlaps = np.zeros((ns, nion, nlm, nlm), dtype=np.float64)
|
|
else:
|
|
ndim = nion * nlm
|
|
occ_mats = np.zeros((ns, 1, ndim, ndim), dtype=np.float64)
|
|
overlaps = np.zeros((ns, 1, ndim, ndim), dtype=np.float64)
|
|
|
|
# self.proj_win = np.zeros((nion, ns, nk, nlm, nb_max), dtype=np.complex128)
|
|
kweights = el_struct.kmesh['kweights']
|
|
occnums = el_struct.ferw
|
|
ib1 = self.ib_min
|
|
ib2 = self.ib_max + 1
|
|
if site_diag:
|
|
for isp in range(ns):
|
|
for ik, weight, occ in zip(it.count(), kweights, occnums[isp, :, :]):
|
|
for io in range(nion):
|
|
proj_k = self.proj_win[io, isp, ik, ...]
|
|
occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
|
|
proj_k.conj().T).real * weight
|
|
overlaps[isp, io, :, :] += np.dot(proj_k,
|
|
proj_k.conj().T).real * weight
|
|
else:
|
|
proj_k = np.zeros((ndim, nbtot), dtype=np.complex128)
|
|
for isp in range(ns):
|
|
for ik, weight, occ in zip(it.count(), kweights, occnums[isp, :, :]):
|
|
for io in range(nion):
|
|
i1 = io * nlm
|
|
i2 = (io + 1) * nlm
|
|
proj_k[i1:i2, :] = self.proj_win[io, isp, ik, ...]
|
|
occ_mats[isp, 0, :, :] += np.dot(proj_k * occ[ib1:ib2],
|
|
proj_k.conj().T).real * weight
|
|
overlaps[isp, 0, :, :] += np.dot(proj_k,
|
|
proj_k.conj().T).real * weight
|
|
|
|
# if not symops is None:
|
|
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
|
|
|
return occ_mats, overlaps
|
|
|
|
################################################################################
|
|
#
|
|
# local_hamiltonian
|
|
#
|
|
################################################################################
|
|
def local_hamiltonian(self, el_struct, site_diag=True, spin_diag=True):
|
|
"""
|
|
Returns occupation matrix/matrices for the shell.
|
|
"""
|
|
nion, ns, nk, nlm, nbtot = self.proj_win.shape
|
|
|
|
assert site_diag, "site_diag = False is not implemented"
|
|
assert spin_diag, "spin_diag = False is not implemented"
|
|
|
|
loc_ham = np.zeros((ns, nion, nlm, nlm), dtype=np.complex128)
|
|
|
|
# self.proj_win = np.zeros((nion, ns, nk, nlm, nb_max), dtype=np.complex128)
|
|
kweights = el_struct.kmesh['kweights']
|
|
occnums = el_struct.ferw
|
|
ib1 = self.ib_min
|
|
ib2 = self.ib_max + 1
|
|
for isp in range(ns):
|
|
for ik, weight, occ, eigk in zip(it.count(), kweights, occnums[isp, :, :],
|
|
el_struct.eigvals[:, ib1:ib2, isp]):
|
|
for io in range(nion):
|
|
proj_k = self.proj_win[io, isp, ik, ...]
|
|
loc_ham[isp, io, :, :] += np.dot(proj_k * (eigk - el_struct.efermi),
|
|
proj_k.conj().T) * weight
|
|
|
|
# if not symops is None:
|
|
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
|
|
|
return loc_ham
|
|
|
|
################################################################################
|
|
#
|
|
# density_of_states
|
|
#
|
|
################################################################################
|
|
def density_of_states(self, el_struct, emesh):
|
|
"""
|
|
Returns projected DOS for the shell.
|
|
"""
|
|
nion, ns, nk, nlm, nbtot = self.proj_win.shape
|
|
|
|
# There is a problem with data storage structure of projectors that will
|
|
# make life more complicated. The problem is that band-indices of projectors
|
|
# for different k-points do not match because we store 'nb_max' values starting
|
|
# from 0.
|
|
nb_max = self.ib_max - self.ib_min + 1
|
|
ns_band = self.ib_win.shape[1]
|
|
|
|
ne = len(emesh)
|
|
dos = np.zeros((ne, ns, nion, nlm))
|
|
w_k = np.zeros((nk, nb_max, ns, nion, nlm), dtype=np.complex128)
|
|
for isp in range(ns):
|
|
for ik in range(nk):
|
|
is_b = min(isp, ns_band)
|
|
ib1 = self.ib_win[ik, is_b, 0]
|
|
ib2 = self.ib_win[ik, is_b, 1] + 1
|
|
for ib_g in range(ib1, ib2):
|
|
for io in range(nion):
|
|
# Note the difference between 'ib' and 'ibn':
|
|
# 'ib' counts from 0 to 'nb_k - 1'
|
|
# 'ibn' counts from 'ib1 - ib_min' to 'ib2 - ib_min'
|
|
ib = ib_g - ib1
|
|
ibn = ib_g - self.ib_min
|
|
proj_k = self.proj_win[io, isp, ik, :, ib]
|
|
w_k[ik, ib, isp, io, :] = proj_k * proj_k.conj()
|
|
|
|
# eigv_ef = el_struct.eigvals[ik, ib, isp] - el_struct.efermi
|
|
itt = el_struct.kmesh['itet'].T
|
|
# k-indices are starting from 0 in Python
|
|
itt[1:, :] -= 1
|
|
for isp in range(ns):
|
|
for ib, eigk in enumerate(el_struct.eigvals[:, self.ib_min:self.ib_max+1, isp].T):
|
|
for ie, e in enumerate(emesh):
|
|
eigk_ef = eigk - el_struct.efermi
|
|
cti = atm.dos_tetra_weights_3d(eigk_ef, e, itt)
|
|
for im in range(nlm):
|
|
for io in range(nion):
|
|
dos[ie, isp, io, im] += np.sum((cti * w_k[itt[1:, :], ib, isp, io, im].real).sum(0) * itt[0, :])
|
|
|
|
dos *= 2 * el_struct.kmesh['volt']
|
|
# for isp in range(ns):
|
|
# for ik, weight, occ in zip(it.count(), kweights, occnums[isp, :, :]):
|
|
# for io in range(nion):
|
|
# proj_k = self.proj_win[isp, io, ik, ...]
|
|
# occ_mats[isp, io, :, :] += np.dot(proj_k * occ[ib1:ib2],
|
|
# proj_k.conj().T).real * weight
|
|
# overlaps[isp, io, :, :] += np.dot(proj_k,
|
|
# proj_k.conj().T).real * weight
|
|
|
|
# if not symops is None:
|
|
# occ_mats = symmetrize_matrix_set(occ_mats, symops, ions, perm_map)
|
|
|
|
return dos
|
|
|
|
################################################################################
|
|
################################################################################
|
|
#
|
|
# class ProjectorShell
|
|
#
|
|
################################################################################
|
|
################################################################################
|
|
class ComplementShell(ProjectorShell):
|
|
"""
|
|
Container of projectors related to a complement shell.
|
|
|
|
|
|
Parameters:
|
|
|
|
- sh_pars (dict) : shell parameters from the config-file
|
|
- proj_compl (numpy.array) : array of complement projectors
|
|
|
|
"""
|
|
def __init__(self, sh_pars, proj_compl, nc_flag):
|
|
self.lorb = sh_pars['lshell']
|
|
self.ions = sh_pars['ions']
|
|
self.user_index = sh_pars['user_index']
|
|
self.corr = sh_pars['corr']
|
|
self.nc_flag = nc_flag
|
|
|
|
self.ib_min = sh_pars['ib_min']
|
|
self.ib_max = sh_pars['ib_max']
|
|
self.ib_win = sh_pars['ib_win']
|
|
|
|
|
|
#self.lm1 = self.lorb**2
|
|
#self.lm2 = (self.lorb+1)**2
|
|
|
|
self.nion = self.ions['nion']
|
|
# Extract ion list and equivalence classes (ion sorts)
|
|
self.ion_list = sorted(it.chain(*self.ions['ion_list']))
|
|
self.ion_sort = []
|
|
for ion in self.ion_list:
|
|
for icl, eq_cl in enumerate(self.ions['ion_list']):
|
|
if ion in eq_cl:
|
|
self.ion_sort.append(icl + 1) # Enumerate classes starting from 1
|
|
break
|
|
|
|
self.ndim = proj_compl.shape[3]
|
|
self.proj_win = proj_compl
|
|
|
|
def extract_tmatrices(self, sh_pars):
|
|
raise Exception('not implemented')
|
|
|
|
def local_hamiltonian(self, el_struct, site_diag=True, spin_diag=True):
|
|
raise Exception('not implemented')
|
|
|
|
def density_matrix(self, el_struct, site_diag=True, spin_diag=True):
|
|
raise Exception('not implemented')
|
|
|
|
#def density_of_states(self, el_struct, emesh):
|
|
# raise Exception('not implemented')
|