fix undefined var names

.github/workflows/python-app.yml

@@ -14,9 +14,7 @@ permissions:
 
 jobs:
  build:
-
  runs-on: ubuntu-latest
-
  steps:
  - uses: actions/checkout@v3
  - name: Set up Python 3.10

TB2J/Oiju_epc.py

@@ -57,13 +57,21 @@ def __init__(
  # prepare dDelta
  self.calc_dDelta()
 
+ self._kmap = None
+
  def prepare_epc_wann(self):
  """
  prepare EPC in electron wannier function representation
  """
  self.EPCmat_wann_up = self.EPCmat_up.to_wann(self.Umat_up)
  self.EPCmat_wann_dn = self.EPCmat_dn.to_wann(self.Umat_dn)
 
+ def get_iq(self, q):
+ if self._kmap is None:
+ self._kmap = {}
+ for i, q in enumerate(self.klist):
+ self._kmap[tuple(q)] = i
+
  def calc_dDelta(self):
  """
  calculate $\delta \Delta$.
@@ -77,7 +85,8 @@ def calc_dDelta(self):
  """
  self.dDelta = np.zeros((self.nphon, self.nwann, self.nwann))
  # iq, iv, iR
- iq0 = iqlist[(0, 0, 0)]
+ # iq0 = self.iqlist[(0, 0, 0)]
+ iq0 = self.get_iq((0, 0, 0))
 
  for iv in range(self.nphon):
  for ik, k in enumerate(self.klist):

TB2J/exchangeCL2.py

@@ -117,17 +117,17 @@ def get_A_ijR(self, Gup, Gdn, iatom, jatom):
  "ij, ji-> ij", np.matmul(Deltai, Gij_up), np.matmul(Deltaj, Gji_dn)
  )
 
- if self.biquadratic:
- A = np.einsum(
- "ij, ji-> ij",
- np.matmul(Deltai, Gij_up),
- np.matmul(Deltaj, Gji_up),
- )
- C = np.einsum(
- "ij, ji-> ij",
- np.matmul(Deltai, Gij_down),
- np.matmul(Deltaj, Gji_down),
- )
+ # if self.biquadratic:
+ # A = np.einsum(
+ # "ij, ji-> ij",
+ # np.matmul(Deltai, Gij_up),
+ # np.matmul(Deltaj, Gji_up),
+ # )
+ # C = np.einsum(
+ # "ij, ji-> ij",
+ # np.matmul(Deltai, Gij_down),
+ # np.matmul(Deltaj, Gji_down),
+ # )
  tmp = np.sum(t)
  self.Jorb_list[(R, iatom, jatom)].append(t / (4.0 * np.pi))
  self.JJ_list[(R, iatom, jatom)].append(tmp / (4.0 * np.pi))

TB2J/exchange_pert.py

@@ -178,19 +178,19 @@ def calculate_all(self):
  """
  print("Green's function Calculation started.")
 
- widgets = [
- " [",
- progressbar.Timer(),
- "] ",
- progressbar.Bar(),
- " (",
- progressbar.ETA(),
- ") ",
- ]
- bar = progressbar.ProgressBar(maxval=self.contour.npoints, widgets=widgets)
- bar.start()
+ # widgets = [
+ # " [",
+ # progressbar.Timer(),
+ # "] ",
+ # progressbar.Bar(),
+ # " (",
+ # progressbar.ETA(),
+ # ") ",
+ # ]
+ # bar = progressbar.ProgressBar(maxval=self.contour.npoints, widgets=widgets)
+ # bar.start()
  for ie in range(self.contour.npoints):
- bar.update(ie)
+ # bar.update(ie)
  e = self.contour.elist[ie]
  de = self.contour.de[ie]
  GR, dGdx = self.G.get_GR_and_dGRdx(self.Rlist, energy=e, dHdx=self.dHdx)
@@ -203,7 +203,7 @@ def calculate_all(self):
  self.A_to_Jtensor()
  if self.calc_NJt:
  self.calculate_DMI_NJT()
- bar.finish()
+ # bar.finish()
 
  def write_output(self, path="TB2J_results"):
  self._prepare_index_spin()

TB2J/exchange_qspace.py

@@ -90,8 +90,8 @@ def get_all_A(self):
  # Kq= Gk_up[ik] @ self.Delta @ Gk_dn[ikq]
  # for ik, ikq in enumerate(range(self.nkpts)):
  Guk = Gk_up[ik, :, :]
- # Gdk = Gk_dn[ik, :, :]
- # Gukq = Gk_up[ikq, :, :]
+ Gdk = Gk_dn[ik, :, :]
+ Gukq = Gk_up[ikq, :, :]
  Gdkq = Gk_dn[ikq, :, :]
  for i, iatom in enumerate(self.ind_mag_atoms):
  Deltai = self.get_Delta(iatom)

TB2J/gpaw_wrapper.py

@@ -61,7 +61,7 @@ def __init__(self, atoms=None, calc=None, gpw_fname=None):
  # return eigh(self.hamk(k), self.S(k))
 
  def get_kpts(self):
- return calc.get_ibz_k_points()
+ return self.calc.get_ibz_k_points()
 
  def HS_and_eigen(self, kpts=None, convention=2):
  if kpts is not None:
@@ -135,7 +135,7 @@ def __init__(self, calc=None, atoms=None, gpw_fname=None, pickle_fname=None):
  self.H_NMM, self.S_NMM = tb.h_and_s()
  self.Rlist = tb.R_cN.T
  else:
- with open(fname, "rb") as myfile:
+ with open(gpw_fname, "rb") as myfile:
  self.H_NMM, self.S_NMM, self.Rlist = pickle.load(myfile)
  self.nR, self.nbasis, _ = self.H_NMM.shape
  self.positions = np.zeros((self.nbasis, 3))

TB2J/mathutils.py

@@ -0,0 +1,12 @@
+import numpy as np
+from scipy.linalg import inv, eigh
+
+
+def Lowdin(S):
+ """
+ Calculate S^(-1/2).
+ Which is used in lowind's symmetric orthonormalization.
+ psi_prime = S^(-1/2) psi
+ """
+ eigval, eigvec = eigh(S)
+ return eigvec @ np.diag(np.sqrt(1.0 / eigval)) @ (eigvec.T.conj())

TB2J/sisl_wrapper.py

@@ -5,6 +5,7 @@
 from collections import defaultdict
 from scipy.linalg import eigh
 from TB2J.myTB import AbstractTB
+from TB2J.mathutils import Lowdin
 
 
 class SislWrapper(AbstractTB):
@@ -199,6 +200,9 @@ def HS_and_eigen(self, kpts, convention=2):
  shape=(nkpts, self.nbasis, self.nbasis),
  dtype=complex,
  )
+ Hk = self.Hk(k, convention=convention)
+ Sk = self.Sk(k, convention=convention)
+ evalue, evec = eigh(Hk, Sk)
  self.H[ik] = Hk
  self.S[ik] = Sk
  self.evals[ik] = evalue

TB2J/spinham/supercell.py

@@ -319,7 +319,7 @@ def map_to_primitive(atoms, primitive_atoms, offset=(0, 0, 0)):
 def test():
  sc_mat = np.diag([1, 1, 2])
  # sc_mat[0, 1] = 2
- spm = supercell_maker(sc_matrix=sc_mat)
+ spm = SupercellMaker(sc_matrix=sc_mat)
  print(spm.sc_cell([1, 1, 1]))
  print(spm.sc_pos([[0.5, 1, 1]]))
  print(spm.sc_trans_invariant(["Fe"]))

TB2J/utils.py

@@ -1,4 +1,5 @@
 from collections import OrderedDict, defaultdict
+import copy
 import numpy as np
 from pathlib import Path