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Lonya0Lonya0
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add manually input overlap matrix feature with example
1 parent 6ba57b4 commit 4a23dca

19 files changed

+477
-31
lines changed

‎dptb/postprocess/elec_struc_cal.py

Lines changed: 24 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,4 @@
11
import os
2-
32
import h5py
43
import numpy as np
54
from ase.io import read
@@ -139,32 +138,34 @@ def get_data(self,
139138
data = data
140139
else:
141140
raise ValueError('data should be either a string, ase.Atoms, or AtomicData')
142-
143-
if device is None:
144-
device = self.device
145-
data = AtomicData.to_AtomicDataDict(data.to(device))
146-
data = self.model.idp(data)
147141

148142
if isinstance(override_overlap, str):
149143
assert os.path.exists(override_overlap), "Overlap file not found."
150144
overlap_blocks = h5py.File(override_overlap, "r")
151145
if len(overlap_blocks) != 1:
152146
log.info('Overlap file contains more than one overlap matrix, only first will be used.')
153-
data[AtomicDataDict.NODE_OVERLAP_KEY] = None
154-
data[AtomicDataDict.EDGE_OVERLAP_KEY] = None
147+
if self.overlap:
148+
log.warning('override_overlap is enabled while model contains overlap, override_overlap will be used.')
155149
if "0" in overlap_blocks:
156150
overlaps = overlap_blocks["0"]
157151
else:
158152
overlaps = overlap_blocks["1"]
159-
block_to_feature(data, self.model.idp, False, overlaps)
160-
self.eigv = Eigenvalues(
161-
idp=self.model.idp,
162-
device=self.device,
163-
s_edge_field=AtomicDataDict.EDGE_OVERLAP_KEY,
164-
s_node_field=AtomicDataDict.NODE_OVERLAP_KEY,
165-
s_out_field=AtomicDataDict.OVERLAP_KEY,
166-
dtype=self.model.dtype,
167-
)
153+
block_to_feature(data, self.model.idp, blocks=False, overlap_blocks=overlaps)
154+
if not self.overlap:
155+
self.eigv = Eigenvalues(
156+
idp=self.model.idp,
157+
device=self.device,
158+
s_edge_field=AtomicDataDict.EDGE_OVERLAP_KEY,
159+
s_node_field=AtomicDataDict.NODE_OVERLAP_KEY,
160+
s_out_field=AtomicDataDict.OVERLAP_KEY,
161+
dtype=self.model.dtype,
162+
)
163+
overlap_blocks.close()
164+
165+
if device is None:
166+
device = self.device
167+
data = AtomicData.to_AtomicDataDict(data.to(device))
168+
data = self.model.idp(data)
168169

169170
return data
170171

@@ -199,8 +200,14 @@ def get_eigs(self,
199200
# set the kpoint of the AtomicData
200201
data[AtomicDataDict.KPOINT_KEY] = \
201202
torch.nested.as_nested_tensor([torch.as_tensor(klist, dtype=self.model.dtype, device=self.device)])
203+
if isinstance(override_overlap, str):
204+
override_overlap_edge = data[AtomicDataDict.EDGE_OVERLAP_KEY]
205+
override_overlap_node = data[AtomicDataDict.NODE_OVERLAP_KEY]
202206
# get the eigenvalues
203207
data = self.model(data)
208+
if isinstance(override_overlap, str):
209+
data[AtomicDataDict.EDGE_OVERLAP_KEY] = override_overlap_edge
210+
data[AtomicDataDict.NODE_OVERLAP_KEY] = override_overlap_node
204211
if self.overlap or isinstance(override_overlap, str):
205212
assert data.get(AtomicDataDict.EDGE_OVERLAP_KEY) is not None
206213
data = self.eigv(data)

‎dptb/tests/data/e3_band/data/Si64.0/atomic_numbers.dat

Lines changed: 64 additions & 0 deletions
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‎dptb/tests/data/e3_band/data/Si64.0/basis.dat

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
{'Si': '1s1p'}

‎dptb/tests/data/e3_band/data/Si64.0/cell.dat

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
1.088740444183349609e+01 0.000000000000000000e+00 0.000000000000000000e+00
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0.000000000000000000e+00 1.088740444183349609e+01 0.000000000000000000e+00
3+
0.000000000000000000e+00 0.000000000000000000e+00 1.088740444183349609e+01

‎dptb/tests/data/e3_band/data/Si64.0/hamiltonians.h5

3.76 MB
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‎dptb/tests/data/e3_band/data/Si64.0/kpoints.npy

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‎dptb/tests/data/e3_band/data/Si64.0/overlaps.h5

2.21 MB
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‎dptb/tests/data/e3_band/data/Si64.0/pbc.dat

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
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1.000000000000000000e+00
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1.000000000000000000e+00
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1.000000000000000000e+00

‎dptb/tests/data/e3_band/data/Si64.0/positions.dat

Lines changed: 64 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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‎dptb/tests/data/e3_band/data/Si64.vasp

Lines changed: 72 additions & 0 deletions
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@@ -0,0 +1,72 @@
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Si64
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Si
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64
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