Add parser for tb.dat

examples/silicon/read_tb.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+# (c) 2015-2018, ETH Zurich, Institut fuer Theoretische Physik
+# Author: Dominik Gresch <[email protected]>
+
+import os
+import shutil
+import subprocess
+import numpy as np
+import tbmodels as tb
+import matplotlib.pyplot as plt
+
+if __name__ == "__main__":
+ WANNIER90_COMMAND = os.path.expanduser("~/git/wannier90/wannier90.x")
+ BUILD_DIR = "./build"
+
+ # shutil.rmtree(BUILD_DIR, ignore_errors=True)
+ # shutil.copytree("./input", BUILD_DIR)
+ # subprocess.call([WANNIER90_COMMAND, "silicon"], cwd=BUILD_DIR)
+
+ # model = tb.Model.from_wannier_folder(BUILD_DIR, prefix="silicon")
+ # print(model)
+ # print(model.hop[(2, 1, -3)])
+
+ BUILD_DIR = "./build2"
+ model = tb.Model.from_wannier_tb_file(
+ tb_file=f'{BUILD_DIR}/silicon_tb.dat',
+ wsvec_file=f'{BUILD_DIR}/silicon_wsvec.dat'
+ )
+ print(model)
+ # print(model.hop[(2, 1, -3)])
+ # exit()
+
+ theta = 37 / 180 * np.pi
+ phi = 43 / 180 * np.pi
+ rlist = np.linspace(0, 2, 20)
+ klist = [[r*np.sin(theta)*np.cos(phi), r*np.sin(theta)*np.sin(phi), r*np.cos(theta)] for r in rlist]
+
+ eigvals = model.eigenval(klist)
+
+ plt.plot(eigvals)
+ plt.show()

tbmodels/_tb_model.py

@@ -531,6 +531,57 @@ def _mat_to_hr(R, mat):
  )
  return lines
 
+ @staticmethod
+ def _read_tb(iterator, ignore_orbital_order=False):
+ """Reads the content of a seedname_tb.dat file"""
+ next(iterator) # skip comment line
+
+ lattice = np.zeros((3, 3))
+ for i in range(3):
+ lattice[i, :] = np.fromstring(next(iterator), sep=' ')
+
+ num_wann = int(next(iterator))
+
+ nrpts = int(next(iterator))
+
+ # degeneracy of Wigner-Seitz grid points, 15 entries per line
+ deg_pts = []
+ # order in zip important because else the next data element is consumed
+ for _, line in zip(range(int(np.ceil(nrpts / 15))), iterator):
+ deg_pts.extend(int(x) for x in line.split())
+ assert len(deg_pts) == nrpts
+
+ # <0n|H|Rm>
+ hop_list = []
+ for ir in range(nrpts):
+ next(iterator) # skip empty
+ r_vec = [int(_) for _ in next(iterator).strip().split()]
+ for j in range(num_wann):
+ for i in range(num_wann):
+ line = next(iterator).strip().split()
+ iw, jw = [int(_) for _ in line[:2]]
+ if not ignore_orbital_order and (iw != i + 1 or jw != j + 1):
+ raise ValueError(f"Inconsistent orbital numbers in line '{line}'")
+ ham = (float(line[2]) + 1j * float(line[3])) / deg_pts[ir]
+ hop_list.append([ham, i, j, r_vec])
+
+ # <0n|r|Rm>
+ r_list = []
+ for ir in range(nrpts):
+ next(iterator) # skip empty
+ r_vec = [int(_) for _ in next(iterator).strip().split()]
+ for j in range(num_wann):
+ for i in range(num_wann):
+ line = next(iterator).strip().split()
+ iw, jw = [int(_) for _ in line[:2]]
+ if not ignore_orbital_order and (iw != i + 1 or jw != j + 1):
+ raise ValueError(f"Inconsistent orbital numbers in line '{line}'")
+ r = np.array([float(_) for _ in line[2:]])
+ r = r[::2] + 1j * r[1::2]
+ r_list.append([r, i, j, r_vec])
+
+ return lattice, num_wann, nrpts, deg_pts, hop_list, r_list
+
  @classmethod
  def from_wannier_folder(
  cls, folder: str = ".", prefix: str = "wannier", **kwargs
@@ -717,6 +768,98 @@ def remap_hoppings(hop_entries):
 
  return cls.from_hop_list(size=num_wann, hop_list=hop_entries, **kwargs)
 
+ @classmethod # noqa: MC0001
+ def from_wannier_tb_file( # pylint: disable=too-many-locals
+ cls,
+ *,
+ tb_file: str,
+ wsvec_file: str,
+ **kwargs,
+ ) -> Model:
+ """
+ Create a :class:`.Model` instance from Wannier90 output files.
+
+ Parameters
+ ----------
+ tb_file :
+ Path of the ``*_tb.dat`` file. Together with the
+ ``*_wsvec.dat`` file, this determines the hopping terms.
+ wsvec_file :
+ Path of the ``*_wsvec.dat`` file. This file determines the
+ remapping of hopping terms when ``use_ws_distance`` is used
+ in the Wannier90 calculation.
+ kwargs :
+ :class:`.Model` keyword arguments.
+ """
+
+ if "uc" in kwargs:
+ raise ValueError(
+ "Ambiguous unit cell: It can be given either via 'uc' or the 'tb_file' keywords, but not both."
+ )
+ if "pos" in kwargs:
+ raise ValueError(
+ "Ambiguous orbital positions: The positions can be given either via the 'pos' or the 'xyz_file' keywords, but not both."
+ )
+
+ with open(tb_file) as f:
+ lattice, num_wann, nrpts, deg_pts, hop_list, r_list = cls._read_tb(f)
+
+ kwargs["uc"] = lattice
+
+ def get_centers(r_list: list) -> list:
+ centers = [None for _ in range(num_wann)]
+ for r, i, j, r_vec in r_list:
+ if r_vec != [0, 0, 0]:
+ continue
+ if i != j:
+ continue
+ r = np.array(r)
+ if not np.allclose(np.abs(r.imag), 0):
+ raise ValueError(f'Center should be real: WF {i+1}, center = {r}')
+ centers[i] = r.real
+ return centers
+
+ pos_cartesian: ty.Union[
+ ty.List[npt.NDArray[np.float_]], npt.NDArray[np.float_]
+ ] = get_centers(r_list)
+
+ kwargs["pos"] = la.solve(kwargs["uc"].T, np.array(pos_cartesian).T).T
+
+ # hop_entries = (hop for hop in hop_entries if abs(hop[0]) > h_cutoff)
+ hop_entries = hop_list
+
+ with open(wsvec_file) as f:
+ wsvec_generator = cls._async_parse(
+ cls._read_wsvec(f), chunksize=num_wann
+ )
+
+ def remap_hoppings(hop_entries):
+ for t, orbital_1, orbital_2, R in hop_entries:
+ # Step _async_parse to where it accepts
+ # a new key.
+ # The _async_parse does not raise StopIteration
+ next( # pylint: disable=stop-iteration-return
+ wsvec_generator
+ )
+ T_list = wsvec_generator.send(
+ (orbital_1, orbital_2, tuple(R))
+ )
+ N = len(T_list)
+ for T in T_list:
+ # not using numpy here increases performance
+ yield (
+ t / N,
+ orbital_1,
+ orbital_2,
+ tuple(r + t for r, t in zip(R, T)),
+ )
+
+ hop_entries = remap_hoppings(hop_entries)
+
+ return cls.from_hop_list(
+ size=num_wann, hop_list=hop_entries, **kwargs
+ )
+
  @staticmethod
  def _async_parse(iterator, chunksize=1):
  """