Coverage for /builds/debichem-team/python-ase/ase/transport/greenfunction.py : 82.50%
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1import numpy as np
4class GreenFunction:
5 """Equilibrium retarded Green function."""
7 def __init__(self, H, S=None, selfenergies=[], eta=1e-4):
8 self.H = H
9 self.S = S
10 self.selfenergies = selfenergies
11 self.eta = eta
12 self.energy = None
13 self.Ginv = np.empty(H.shape, complex)
15 def retarded(self, energy, inverse=False):
16 """Get retarded Green function at specified energy.
18 If 'inverse' is True, the inverse Green function is returned (faster).
19 """
20 if energy != self.energy:
21 self.energy = energy
22 z = energy + self.eta * 1.j
24 if self.S is None:
25 self.Ginv[:] = 0.0
26 self.Ginv.flat[:: len(self.S) + 1] = z
27 else:
28 self.Ginv[:] = z
29 self.Ginv *= self.S
30 self.Ginv -= self.H
32 for selfenergy in self.selfenergies:
33 self.Ginv -= selfenergy.retarded(energy)
35 if inverse:
36 return self.Ginv
37 else:
38 return np.linalg.inv(self.Ginv)
40 def calculate(self, energy, sigma):
41 """XXX is this really needed"""
42 ginv = energy * self.S - self.H - sigma
43 return np.linalg.inv(ginv)
45 def apply_retarded(self, energy, X):
46 """Apply retarded Green function to X.
48 Returns the matrix product G^r(e) . X
49 """
50 return np.linalg.solve(self.retarded(energy, inverse=True), X)
52 def dos(self, energy):
53 """Total density of states -1/pi Im(Tr(GS))"""
54 if self.S is None:
55 return -self.retarded(energy).imag.trace() / np.pi
56 else:
57 GS = self.apply_retarded(energy, self.S)
58 return -GS.imag.trace() / np.pi
60 def pdos(self, energy):
61 """Projected density of states -1/pi Im(SGS/S)"""
62 if self.S is None:
63 return -self.retarded(energy).imag.diagonal() / np.pi
64 else:
65 S = self.S
66 SGS = np.dot(S, self.apply_retarded(energy, S))
67 return -(SGS.diagonal() / S.diagonal()).imag / np.pi