remove charge-scaling traj-2 and update tutorial

Author: Chun Kei (Tom) Lam

pyproject.toml

@@ -5,6 +5,8 @@ description = "Toolkit for Analysis of Permeation Cycles in Potassium Channels"
 authors = ["Chun Kei (Tom) Lam <[email protected]>"]
 license = "GPL-3.0"
 readme = "README.md"
+include = ["CHANGELOG.md"]
+
 
 [tool.poetry.dependencies]
 python = ">=3.8, <3.12"
@@ -20,11 +22,6 @@ jupyter = "^1.0.0"
 pytest = "^7.3.1"
 
 
-[[tool.poetry.source]]
-name = "foo"
-url = "https://test.pypi.org/"
-priority = "supplemental"
-
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

tutorials/charge-scaling/charge-scaling.ipynb

@@ -565,7 +565,6 @@
 139 42111 48.62000 2
 139 42120 43.63000 4
 139 42052 39.31000 5
-140 42043 57.77000 0
 140 42144 53.01000 1
 140 42111 49.58000 2
 140 42120 44.03000 4
@@ -915,7 +914,6 @@
 227 42120 49.09000 2
 227 42143 45.81001 3
 227 42070 42.10000 4
-228 42102 58.52000 0
 228 42111 53.84000 1
 228 42120 50.73000 2
 228 42143 47.46000 3
@@ -960,7 +958,6 @@
 237 42143 48.20000 2
 237 42070 42.96000 4
 237 42095 39.21000 5
-238 42111 57.28000 0
 238 42120 52.65000 1
 238 42143 49.00000 2
 238 42070 43.99000 4

tutorials/charge-scaling/traj-0/k_in_sf.dat

@@ -1,18 +1,21 @@
 =================================
-Total time: 5.000000 ns
-dt: 0.020000 ns
+Total time: 5.000 ns
+dt: 0.0200 ns
 Number of K+: 148
 Number of water: 7272
-Number of net ion permeation events (jump) = 3
-Number of net water permeation events (jump) = 0
-Current (jump) = 96.11999999999999 pA
+
 Number of upward ion permeation events (cross) = 22
 Number of downward ion permeation events (cross) = 18
 Number of net ion permeation events (cross) = 4
 Number of upward water permeation events (cross) = 0
 Number of downward water permeation events (cross) = 0
 Number of net water permeation events (cross) = 0
-Ion Current (cross) = 128.16 pA
+K+ current (cross) = 128.16 pA
+
+Number of net ion permeation events (jump) = 3
+Number of net water permeation events (jump) = 0
+K+ current (jump) = 96.12 pA
+
 Results saved to /home/clam/projects/Markov/softs/KPerm/tutorials/charge-scaling/traj-0/kperm.csv
 Log saved to /home/clam/projects/Markov/softs/KPerm/tutorials/charge-scaling/traj-0/kperm.log
 =================================