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katdueckerasoplata
katduecker
authored and
asoplata
committed
fix: add missing "v" read-in (with back-compat)
This also includes regenerated networks, since doing that is necessary to allow the tests to pass as well. The original person who actually wrote this code was @katduecker, which is why they are indicated as author. This version of the code that was extracted from jonescompneurolab#1168 was done so by @asoplata .
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3 files changed

+57
-7
lines changed

3 files changed

+57
-7
lines changed

‎hnn_core/hnn_io.py‎

Lines changed: 19 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -166,13 +166,25 @@ def _read_cell_types(cell_types_data):
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sections_data = cell_data["sections"]
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for section_name in sections_data:
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section_data = sections_data[section_name]
169-
sections[section_name] = Section(
170-
L=section_data["L"],
171-
diam=section_data["diam"],
172-
cm=section_data["cm"],
173-
Ra=section_data["Ra"],
174-
end_pts=section_data["end_pts"],
175-
)
169+
if "v" in section_data.keys():
170+
sections[section_name] = Section(
171+
L=section_data["L"],
172+
diam=section_data["diam"],
173+
cm=section_data["cm"],
174+
Ra=section_data["Ra"],
175+
v=section_data["v"],
176+
end_pts=section_data["end_pts"],
177+
)
178+
else:
179+
# Yet more legacy backwards-compatibility
180+
sections[section_name] = Section(
181+
L=section_data["L"],
182+
diam=section_data["diam"],
183+
cm=section_data["cm"],
184+
Ra=section_data["Ra"],
185+
end_pts=section_data["end_pts"],
186+
)
187+
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# Set section attributes
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sections[section_name].syns = section_data["syns"]
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sections[section_name].mechs = section_data["mechs"]

‎hnn_core/param/jones2009_base.json‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@
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]
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],
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"nseg": 1,
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"v": -65,
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"mechs": {
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"hh2": {}
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},
@@ -110,6 +111,7 @@
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]
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],
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"nseg": 1,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -146,6 +148,7 @@
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]
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],
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"nseg": 7,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -182,6 +185,7 @@
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]
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],
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"nseg": 5,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -218,6 +222,7 @@
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]
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],
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"nseg": 7,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -254,6 +259,7 @@
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]
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],
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"nseg": 1,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -290,6 +296,7 @@
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]
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],
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"nseg": 5,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -326,6 +333,7 @@
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]
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],
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"nseg": 5,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -362,6 +370,7 @@
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]
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],
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"nseg": 1,
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"v": -65,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -494,6 +503,7 @@
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]
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],
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"nseg": 1,
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"v": -65,
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"mechs": {
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"hh2": {}
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},
@@ -570,6 +580,7 @@
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]
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],
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"nseg": 3,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -632,6 +643,7 @@
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]
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],
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"nseg": 13,
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"v": -71.32,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -714,6 +726,7 @@
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]
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],
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"nseg": 13,
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"v": -69.08,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -796,6 +809,7 @@
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]
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],
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"nseg": 9,
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"v": -67.3,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -870,6 +884,7 @@
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]
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],
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"nseg": 5,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -936,6 +951,7 @@
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]
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],
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"nseg": 1,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -994,6 +1010,7 @@
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]
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],
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"nseg": 5,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -1060,6 +1077,7 @@
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]
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],
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"nseg": 5,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -1126,6 +1144,7 @@
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]
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],
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"nseg": 1,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,

‎hnn_core/tests/assets/jones2009_3x3_drives.json‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,7 @@
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]
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],
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"nseg": 1,
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"v": -65,
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"mechs": {
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"hh2": {}
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},
@@ -110,6 +111,7 @@
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]
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],
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"nseg": 1,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -146,6 +148,7 @@
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]
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],
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"nseg": 7,
151+
"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -182,6 +185,7 @@
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]
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],
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"nseg": 5,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -218,6 +222,7 @@
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]
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],
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"nseg": 7,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -254,6 +259,7 @@
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]
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],
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"nseg": 1,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -290,6 +296,7 @@
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]
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],
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"nseg": 5,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -326,6 +333,7 @@
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]
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],
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"nseg": 5,
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"v": -71.46,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -362,6 +370,7 @@
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]
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],
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"nseg": 1,
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"v": -65,
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"mechs": {
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"km": {
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"gbar_km": 250.0
@@ -494,6 +503,7 @@
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]
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],
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"nseg": 1,
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"v": -65,
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"mechs": {
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"hh2": {}
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},
@@ -570,6 +580,7 @@
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]
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],
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"nseg": 3,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -632,6 +643,7 @@
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]
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],
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"nseg": 13,
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"v": -71.32,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -714,6 +726,7 @@
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]
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],
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"nseg": 13,
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"v": -69.08,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -796,6 +809,7 @@
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]
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],
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"nseg": 9,
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"v": -67.3,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -870,6 +884,7 @@
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]
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],
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"nseg": 5,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -936,6 +951,7 @@
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]
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],
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"nseg": 1,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -994,6 +1010,7 @@
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]
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],
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"nseg": 5,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -1060,6 +1077,7 @@
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]
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],
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"nseg": 5,
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"v": -72,
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"mechs": {
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"hh2": {
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"gkbar_hh2": 0.01,
@@ -1126,6 +1144,7 @@
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]
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],
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"nseg": 1,
1147+
"v": -72,
11291148
"mechs": {
11301149
"hh2": {
11311150
"gkbar_hh2": 0.01,

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