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Interface refactoring

Merged Interface refactoring
interface-refactoring into main
Merged Kostas Vilkelis requested to merge interface-refactoring into main
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codes/utils.py → codes/kwant_helper/utils.py
+ 152
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import numpy as np
import kwant
from scipy.sparse import coo_array
from itertools import product
import inspect
from copy import copy
from itertools import product
def get_fermi_energy(vals, filling):
"""
Compute Fermi energy for a given filling factor.
vals : nd-array
Collection of eigenvalues on a grid.
filling : int
Number of electrons per cell.
"""
norbs = vals.shape[-1]
vals_flat = np.sort(vals.flatten())
ne = len(vals_flat)
ifermi = int(round(ne * filling / norbs))
if ifermi >= ne:
return vals_flat[-1]
elif ifermi == 0:
return vals_flat[0]
else:
fermi = (vals_flat[ifermi - 1] + vals_flat[ifermi]) / 2
return fermi
import kwant
import numpy as np
from scipy.sparse import coo_array
def builder2tb_model(builder, params={}, return_data=False):
"""
Constructs a tight-binding model dictionary from a `kwant.Builder`.
def builder_to_tb(builder, params={}, return_data=False):
"""Construct a tight-binding model dictionary from a `kwant.Builder`.
Parameters:
-----------
Parameters
----------
builder : `kwant.Builder`
Either builder for non-interacting system or interacting Hamiltonian.
params : dict
@@ -41,9 +19,9 @@ def builder2tb_model(builder, params={}, return_data=False):
return_data : bool
Returns dictionary with sites and number of orbitals per site.
Returns:
--------
tb_model : dict
Returns
-------
h_0 : dict
Tight-binding model of non-interacting systems.
data : dict
Data with sites and number of orbitals. Only if `return_data=True`.
@@ -52,7 +30,7 @@ def builder2tb_model(builder, params={}, return_data=False):
# Extract information from builder
dims = len(builder.symmetry.periods)
onsite_idx = tuple([0] * dims)
tb_model = {}
h_0 = {}
sites_list = [*builder.sites()]
norbs_list = [site[0].norbs for site in builder.sites()]
positions_list = [site[0].pos for site in builder.sites()]
@@ -73,14 +51,14 @@ def builder2tb_model(builder, params={}, return_data=False):
_params[arg] = params[arg]
val = val(site, **_params)
data = val.flatten()
except:
except Exception:
data = val.flatten()
if onsite_idx in tb_model:
tb_model[onsite_idx] += coo_array(
if onsite_idx in h_0:
h_0[onsite_idx] += coo_array(
(data, (row, col)), shape=(norbs_tot, norbs_tot)
).toarray()
else:
tb_model[onsite_idx] = coo_array(
h_0[onsite_idx] = coo_array(
(data, (row, col)), shape=(norbs_tot, norbs_tot)
).toarray()
# Hopping matrices
@@ -101,146 +79,58 @@ def builder2tb_model(builder, params={}, return_data=False):
_params[arg] = params[arg]
val = val(a, b, **_params)
data = val.flatten()
except:
except Exception:
data = val.flatten()
if tuple(b_dom) in tb_model:
tb_model[tuple(b_dom)] += coo_array(
if tuple(b_dom) in h_0:
h_0[tuple(b_dom)] += coo_array(
(data, (row, col)), shape=(norbs_tot, norbs_tot)
).toarray()
if np.linalg.norm(b_dom) == 0:
tb_model[tuple(b_dom)] += (
h_0[tuple(b_dom)] += (
coo_array((data, (row, col)), shape=(norbs_tot, norbs_tot))
.toarray()
.T.conj()
)
else:
# Hopping vector in the opposite direction
tb_model[tuple(-b_dom)] += coo_array(
(data, (row, col)), shape=(norbs_tot, norbs_tot)
).toarray().T.conj()
h_0[tuple(-b_dom)] += (
coo_array((data, (row, col)), shape=(norbs_tot, norbs_tot))
.toarray()
.T.conj()
)
else:
tb_model[tuple(b_dom)] = coo_array(
h_0[tuple(b_dom)] = coo_array(
(data, (row, col)), shape=(norbs_tot, norbs_tot)
).toarray()
if np.linalg.norm(b_dom) == 0:
tb_model[tuple(b_dom)] += (
h_0[tuple(b_dom)] += (
coo_array((data, (row, col)), shape=(norbs_tot, norbs_tot))
.toarray()
.T.conj()
)
else:
tb_model[tuple(-b_dom)] = coo_array(
(data, (row, col)), shape=(norbs_tot, norbs_tot)
).toarray().T.conj()
h_0[tuple(-b_dom)] = (
coo_array((data, (row, col)), shape=(norbs_tot, norbs_tot))
.toarray()
.T.conj()
)
if return_data:
data = {}
data["norbs"] = norbs_list
data["positions"] = positions_list
return tb_model, data
return h_0, data
else:
return tb_model
def model2hk(tb_model):
"""
Build Bloch Hamiltonian.
Paramters:
----------
nk : int
Number of k-points along each direction.
tb_model : dictionary
Must have the following structure:
- Keys are tuples for each hopping vector (in units of lattice vectors).
- Values are hopping matrices.
return_ks : bool
Return k-points.
Returns:
--------
ham : nd.array
Hamiltonian evaluated on a k-point grid from k-points
along each direction evaluated from zero to 2*pi.
The indices are ordered as [k_1, ... , k_n, i, j], where
`k_m` corresponding to the k-point element along each
direction and `i` and `j` are the internal degrees of freedom.
ks : 1D-array
List of k-points over all directions. Only returned if `return_ks=True`.
Returns:
--------
bloch_ham : function
Evaluates the Hamiltonian at a given k-point.
"""
assert (
len(next(iter(tb_model))) > 0
), "Zero-dimensional system. The Hamiltonian is simply tb_model[()]."
def bloch_ham(k):
ham = 0
for vector in tb_model.keys():
ham += tb_model[vector] * np.exp(
-1j * np.dot(k, np.array(vector, dtype=float))
)
return ham
return bloch_ham
return h_0
def kgrid_hamiltonian(nk, hk, dim, return_ks=False, hermitian=True):
"""
Evaluates Hamiltonian on a k-point grid.
def build_interacting_syst(builder, func_onsite, func_hop, max_neighbor=1):
"""Construct an auxiliary `kwant` system to build Hamiltonian matrix.
Paramters:
Parameters
----------
nk : int
Number of k-points along each direction.
hk : function
Calculates the Hamiltonian at a given k-point.
return_ks : bool
If `True`, returns k-points.
Returns:
--------
ham : nd.array
Hamiltonian evaluated on a k-point grid from k-points
along each direction evaluated from zero to 2*pi.
The indices are ordered as [k_1, ... , k_n, i, j], where
`k_m` corresponding to the k-point element along each
direction and `i` and `j` are the internal degrees of freedom.
ks : 1D-array
List of k-points over all directions. Only returned if `return_ks=True`.
"""
ks = 2 * np.pi * np.linspace(0, 1, nk, endpoint=False)
k_pts = np.tile(ks, dim).reshape(dim, nk)
ham = []
for k in product(*k_pts):
ham.append(hk(k))
ham = np.array(ham)
if hermitian:
assert np.allclose(
ham, np.transpose(ham, (0, 2, 1)).conj()
), "Tight-binding provided is non-Hermitian. Not supported yet"
shape = (*[nk] * dim, ham.shape[-1], ham.shape[-1])
if return_ks:
return ham.reshape(*shape), ks
else:
return ham.reshape(*shape)
def build_interacting_syst(builder, lattice, func_onsite, func_hop, max_neighbor=1):
"""
Construct an auxiliary `kwant` system to build Hamiltonian matrix.
Parameters:
-----------
builder : `kwant.Builder`
Non-interacting `kwant` system.
lattice : `kwant.lattice`
System lattice.
func_onsite : function
Onsite function.
func_hop : function
@@ -248,177 +138,15 @@ def build_interacting_syst(builder, lattice, func_onsite, func_hop, max_neighbor
max_neighbor : int
Maximal nearest-neighbor order.
Returns:
--------
Returns
-------
int_builder : `kwant.Builder`
Dummy `kwant.Builder` to compute interaction matrix.
"""
lattice_info = list(builder.sites())[0][0]
lattice = kwant.lattice.general(lattice_info.prim_vecs, norbs=lattice_info.norbs)
int_builder = kwant.Builder(kwant.TranslationalSymmetry(*builder.symmetry.periods))
int_builder[builder.sites()] = func_onsite
for neighbors in range(max_neighbor):
int_builder[lattice.neighbors(neighbors + 1)] = func_hop
return int_builder
def generate_guess(vectors, ndof, scale=0.1):
"""
vectors : list
List of hopping vectors.
ndof : int
Number internal degrees of freedom (orbitals),
scale : float
The scale of the guess. Maximum absolute value of each element of the guess.
Returns:
--------
guess : nd-array
Guess evaluated on a k-point grid.
"""
guess = {}
for vector in vectors:
if vector not in guess.keys():
amplitude = scale * np.random.rand(ndof, ndof)
phase = 2 * np.pi * np.random.rand(ndof, ndof)
rand_hermitian = amplitude * np.exp(1j * phase)
if np.linalg.norm(np.array(vector)) == 0:
rand_hermitian += rand_hermitian.T.conj()
rand_hermitian /= 2
guess[vector] = rand_hermitian
else:
guess[vector] = rand_hermitian
guess[tuple(-np.array(vector))] = rand_hermitian.T.conj()
return guess
def generate_vectors(cutoff, dim):
"""
Generates hopping vectors up to a cutoff.
Parameters:
-----------
cutoff : int
Maximum distance along each direction.
dim : int
Dimension of the vectors.
Returns:
--------
List of hopping vectors.
"""
return [*product(*([[*range(-cutoff, cutoff + 1)]] * dim))]
def hk2tb_model(hk, hopping_vecs, ks=None):
"""
Extract hopping matrices from Bloch Hamiltonian.
Parameters:
-----------
hk : nd-array
Bloch Hamiltonian matrix hk[k_x, ..., k_n, i, j]
tb_model : dict
Tight-binding model of non-interacting systems.
int_model : dict
Tight-binding model for interacting Hamiltonian.
ks : 1D-array
Set of k-points. Repeated for all directions. If the system is finite, `ks=None`.
Returns:
--------
scf_model : dict
TIght-binding model of Hartree-Fock solution.
"""
if ks is not None:
ndim = len(hk.shape) - 2
dk = np.diff(ks)[0]
nk = len(ks)
k_pts = np.tile(ks, ndim).reshape(ndim, nk)
k_grid = np.array(np.meshgrid(*k_pts))
k_grid = k_grid.reshape(k_grid.shape[0], np.prod(k_grid.shape[1:]))
hk = hk.reshape(np.prod(hk.shape[:ndim]), *hk.shape[-2:])
hopps = (
np.einsum(
"ij,jkl->ikl",
np.exp(1j * np.einsum("ij,jk->ik", hopping_vecs, k_grid)),
hk,
)
* (dk / (2 * np.pi)) ** ndim
)
tb_model = {}
for i, vector in enumerate(hopping_vecs):
tb_model[tuple(vector)] = hopps[i]
return tb_model
else:
return {(): hk}
def calc_gap(vals, E_F):
"""
Compute gap.
Parameters:
-----------
vals : nd-array
Eigenvalues on a k-point grid.
E_F : float
Fermi energy.
Returns:
--------
gap : float
Indirect gap.
"""
emax = np.max(vals[vals <= E_F])
emin = np.min(vals[vals > E_F])
return np.abs(emin - emax)
def matrix_to_flat(matrix):
"""
Flatten the upper triangle of a collection of matrices.
Parameters:
-----------
matrix : nd-array
Array with shape (..., n, n)
"""
return matrix[..., *np.triu_indices(matrix.shape[-1])].flatten()
def flat_to_matrix(flat, shape):
"""
Undo `matrix_to_flat`.
Parameters:
-----------
flat : 1d-array
Output from `matrix_to_flat`.
shape : 1d-array
Shape of the input from `matrix_to_flat`.
"""
matrix = np.zeros(shape, dtype=complex)
matrix[..., *np.triu_indices(shape[-1])] = flat.reshape(*shape[:-2], -1)
indices = np.arange(shape[-1])
diagonal = matrix[..., indices, indices]
matrix += np.moveaxis(matrix, -1, -2).conj()
matrix[..., indices, indices] -= diagonal
return matrix
def complex_to_real(z):
"""
Split real and imaginary parts of a complex array.
Parameters:
-----------
z : array
"""
return np.concatenate((np.real(z), np.imag(z)))
def real_to_complex(z):
"""
Undo `complex_to_real`.
"""
return z[:len(z)//2] + 1j * z[len(z)//2:]
\ No newline at end of file