def write_output(self, path='TB2J_results'):
self._prepare_index_spin()
output = SpinIO(
atoms=self.atoms,
charges=self.charges,
spinat=self.spinat,
index_spin=self.index_spin,
colinear=True,
distance_dict=self.distance_dict,
exchange_Jdict=self.exchange_Jdict,
dmi_ddict=None,
NJT_Jdict=None,
NJT_ddict=None,
biquadratic_Jdict=self.B,
)
output.write_all(path=path)
def write_output(self, path='TB2J_results'):
self._prepare_index_spin()
output = SpinIO(
atoms=self.atoms,
charges=self.charges,
spinat=self.spinat,
index_spin=self.index_spin,
colinear=False,
distance_dict=self.distance_dict,
exchange_Jdict=self.exchange_Jdict,
dmi_ddict=self.DMI,
NJT_Jdict=self.Jdict_NJT,
NJT_ddict=self.Ddict_NJT,
Jani_dict=self.Jani,
biquadratic_Jdict=self.B,
debug_dict=self.debug_dict,
description=self.description,
)
output.write_all(path=path)
def write_output(self, path='TB2J_results'):
self._prepare_index_spin()
output = SpinIO(
atoms=self.atoms,
charges=self.charges,
spinat=self.spinat,
index_spin=self.index_spin,
colinear=True,
orbital_names=self.orbital_names,
distance_dict=self.distance_dict,
exchange_Jdict=self.exchange_Jdict,
Jiso_orb=self.Jiso_orb,
dmi_ddict=None,
NJT_Jdict=None,
NJT_ddict=None,
Jani_dict=None,
biquadratic_Jdict=None,
description=self.description,
)
output.write_all(path=path)
def __init__(self, inpath, metals, ligands, outpath):
fname = os.path.join(inpath, 'TB2J.pickle')
with open(fname, 'rb') as myfile:
self.obj = pickle.load(myfile)
self.atoms = self.obj['atoms']
self.magnetic_elements = metals
self.iM = []
self.iL = []
for i, sym in enumerate(self.atoms.get_chemical_symbols()):
if sym in self.magnetic_elements:
self.iM.append(i)
elif sym in ligands:
self.iL.append(i)
self.ind_mag_atoms = self.iM
self.nM = len(self.iM)
self.nL = len(self.iL)
self.nsite = self.nM + self.nL
atoms = self.obj['atoms']
index_spin = self.obj['index_spin']
ind_atoms = self.obj['ind_atoms']
Jdict = self.obj['exchange_Jdict']
nspin = len(index_spin)
JR = defaultdict(lambda: np.zeros((nspin, nspin), dtype=float))
for key, val in Jdict.items():
R, i, j = key
JR[R][i, j] = val
Rlist = list(JR.keys())
# build matrix form of JR
nR = len(Rlist)
JR2 = np.zeros((nR, nspin, nspin), dtype=float)
for i, (key, val) in enumerate(JR.items()):
JR2[i] = val
# sum rule
iR0 = np.argmin(np.linalg.norm(Rlist, axis=1))
for i in range(self.nsite):
sum_JRi = np.sum(np.sum(JR2, axis=0)[i])
JR2[iR0][i, i] -= sum_JRi
d = JDownfolder(JR2, Rlist, iM=self.iM, iL=self.iL, qmesh=[7, 7, 7])
Jd = d.get_JR()
self.Rlist = Rlist
self.Rcut = None
self._prepare_distance()
self._prepare_index_spin()
self.Jdict = {}
for iR, R in enumerate(d.Rlist):
for i, ispin in enumerate(self.index_spin):
for j, jspin in enumerate(self.index_spin):
if ispin >= 0 and jspin >= 0:
self.Jdict[(tuple(R), i, j)] = Jd[iR, i, j]
io = SpinIO(atoms=atoms,
spinat=self.obj['spinat'],
charges=self.obj['charges'],
index_spin=self.index_spin,
colinear=True,
distance_dict=self.distance_dict,
exchange_Jdict=self.Jdict)
io.write_all(outpath)