remove O1->I1 6k transition

Author: AdrianBeersingVasquez

pyrho/models.py

@@ -849,20 +849,23 @@ class RhO_6Kstates(RhodopsinModel):
     paramsList = ['g0', 'gam', 'phi_m', 'k1', 'k2', 'p',
                   'Gf0', 'k_f', 'q', 'Go1', 'Go2',
                   'Ga3', 'Gd1', 'Gd2', 'Gb', 'E', 'v0', 'v1']  # List of model constants
-
-#    connect = [[0, 0, 1, 1, 0, 1],  # s_1 --> s_i=1...6
-#               [1, 0, 1, 0, 0, 0],  # s_2 -->
-#               [0, 1, 0, 0, 0, 0],
-#               [0, 0, 0, 0, 1, 0],
-#               [0, 0, 0, 0, 0, 1],
-#               [1, 0, 0, 1, 0, 0]]
-    
-    connect = [[0, 1, 0, 0, 0, 1],  # s_1 --> s_i=1...6
-               [0, 0, 1, 0, 0, 0],  # s_2 -->
-               [1, 1, 0, 0, 0, 0],
-               [1, 0, 0, 0, 0, 1],
-               [0, 0, 0, 1, 0, 0],
-               [1, 0, 0, 0, 1, 0]]
+                  # Assuming Gb is constant (not flux-dependent) Gb0 and k_b not needed
+
+# With the O1-> I1 transition
+#     connect = [[0, 1, 0, 0, 0, 1],  # s_1 --> s_i=1...6
+#               [0, 0, 1, 0, 0, 0],  # s_2 -->
+#               [1, 1, 0, 0, 0, 0],
+#               [1, 0, 0, 0, 0, 1],
+#               [0, 0, 0, 1, 0, 0],
+#               [1, 0, 0, 0, 1, 0]]
+
+    # Withouth O1->I1 transition
+    connect = [[0, 1, 0, 0, 0, 1],  # C1 -> I1, C2
+               [0, 0, 1, 0, 0, 0],  # I1 -> O1
+               [1, 0, 0, 0, 0, 0],  # O1 -> C1
+               [1, 0, 0, 0, 0, 1],  # O2 -> C1, C2
+               [0, 0, 0, 1, 0, 0],  # I2 -> O2
+               [1, 0, 0, 0, 1, 0]]  # C2 -> C1, I2
 
     equations = r"""
                 $$ \dot{C_1} = G_{d1}O_1 + G_{b}C_2 + G_{a3}O_2 - G_{a1}(\phi)C_1 - G_{f}(\phi)C_1 $$