Add test for tb.dat

examples/silicon/.gitignore

@@ -1 +1,2 @@
 build
+build_tb

examples/silicon/read_tb.py

@@ -1,8 +1,5 @@
 #!/usr/bin/env python
-
-# (c) 2015-2018, ETH Zurich, Institut fuer Theoretische Physik
-# Author: Dominik Gresch <[email protected]>
-
+# Construct a Model from wannier90 tb.dat file.
 import os
 import shutil
 import subprocess
@@ -12,29 +9,30 @@
 
 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)
+ BUILD_DIR = "./build_tb"
 
- # model = tb.Model.from_wannier_folder(BUILD_DIR, prefix="silicon")
- # print(model)
- # print(model.hop[(2, 1, -3)])
+ if not os.path.exists(BUILD_DIR):
+  shutil.copytree("./input", BUILD_DIR)
+  subprocess.call([WANNIER90_COMMAND, "silicon"], cwd=BUILD_DIR)
 
- 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'
+ model = tb.Model.from_wannier_tb_files(
+ 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()
 
+ # Compute band structure along an arbitrary kpath
  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]
+ 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)
 

tbmodels/_tb_model.py

@@ -538,7 +538,7 @@ def _read_tb(iterator, ignore_orbital_order=False):
 
  lattice = np.zeros((3, 3))
  for i in range(3):
- lattice[i, :] = np.fromstring(next(iterator), sep=' ')
+ lattice[i, :] = np.fromstring(next(iterator), sep=" ")
 
  num_wann = int(next(iterator))
 
@@ -554,28 +554,32 @@ def _read_tb(iterator, ignore_orbital_order=False):
  # <0n|H|Rm>
  hop_list = []
  for ir in range(nrpts):
- next(iterator) # skip empty
+ 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}'")
+ 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
+ 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}'")
+ 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])
@@ -769,7 +773,7 @@ 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
+ def from_wannier_tb_files( # pylint: disable=too-many-locals
  cls,
  *,
  tb_file: str,
@@ -803,19 +807,19 @@ def from_wannier_tb_file( # pylint: disable=too-many-locals
 
  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)]
+ def get_centers(r_list: ty.List[ty.Any]) -> ty.List[npt.NDArray[np.float_]]:
+ centers = [np.zeros(3) 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}')
+ raise ValueError(f"Center should be real: WF {i+1}, center = {r}")
  centers[i] = r.real
  return centers
 
@@ -829,21 +833,15 @@ def get_centers(r_list: list) -> list:
  hop_entries = hop_list
 
  with open(wsvec_file) as f:
- wsvec_generator = cls._async_parse(
- cls._read_wsvec(f), chunksize=num_wann
- )
+ 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))
- )
+ next(wsvec_generator) # pylint: disable=stop-iteration-return
+ 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
@@ -856,9 +854,7 @@ def remap_hoppings(hop_entries):
 
  hop_entries = remap_hoppings(hop_entries)
 
- return cls.from_hop_list(
- size=num_wann, hop_list=hop_entries, **kwargs
- )
+ return cls.from_hop_list(size=num_wann, hop_list=hop_entries, **kwargs)
 
  @staticmethod
  def _async_parse(iterator, chunksize=1):