Fixes for cantata (#2438)

thorstenhater · web-flow · commit 79983144e6f2 · 2025-02-12T14:27:41.000+01:00
- bind the correct class `py_ion_data`
- use `LOCAL`  conductances.
diff --git a/mechanisms/allen/K_T.mod b/mechanisms/allen/K_T.mod
@@ -29,7 +29,9 @@ STATE {
 
 BREAKPOINT {
     SOLVE states METHOD cnexp
-    ik = gbar*m*m*m*m*h*(v-ek)
+    LOCAL g
+    g = gbar*m*m*m*m*h
+    ik = g*(v-ek)
 }
 
 DERIVATIVE states {
diff --git a/mechanisms/allen/Kd.mod b/mechanisms/allen/Kd.mod
@@ -23,7 +23,9 @@ STATE {
 
 BREAKPOINT {
    SOLVE states METHOD cnexp
-   ik = gbar*m*h*(v - ek)
+   LOCAL g
+   g = gbar*m*h
+   ik = g*(v - ek)
 }
 
 DERIVATIVE states {
diff --git a/mechanisms/allen/Kv3_1.mod b/mechanisms/allen/Kv3_1.mod
@@ -23,7 +23,9 @@ STATE {
 
 BREAKPOINT {
     SOLVE states METHOD cnexp
-    ik = gbar*m*(v - ek)
+    LOCAL g
+    g = gbar*m
+    ik = g*(v - ek)
 }
 
 DERIVATIVE states {
diff --git a/python/cells.cpp b/python/cells.cpp
@@ -600,7 +600,7 @@ void register_cells(py::module& m) {
         .def_readonly("diffusivity",            &arb::cable_cell_ion_data::diffusivity,             "Diffusivity.")
         .def_readonly("reversal_concentration", &arb::cable_cell_ion_data::init_reversal_potential, "Reversal potential.");
 
-    ion_data
+    py_ion_data
         .def_property_readonly("charge",                    [](const ion_settings& s) { return s.charge; },                    "Valence.")
         .def_property_readonly("internal_concentration",    [](const ion_settings& s) { return s.internal_concentration; },    "Internal concentration.")
         .def_property_readonly("external_concentration",    [](const ion_settings& s) { return s.external_concentration; },    "External concentration.")

Original file line number	Diff line number	Diff line change
`@@ -29,7 +29,9 @@ STATE {`
`29`	`29`
`30`	`30`	`BREAKPOINT {`
`31`	`31`	`SOLVE states METHOD cnexp`
`32`		`- ik = gbarmmmmh(v-ek)`
	`32`	`+ LOCAL g`
	`33`	`+ g = gbarmmmm*h`
	`34`	`+ ik = g*(v-ek)`
`33`	`35`	`}`
`34`	`36`
`35`	`37`	`DERIVATIVE states {`
Original file line number	Diff line number	Diff line change
`@@ -23,7 +23,9 @@ STATE {`
`23`	`23`
`24`	`24`	`BREAKPOINT {`
`25`	`25`	`SOLVE states METHOD cnexp`
`26`		`- ik = gbarmh*(v - ek)`
	`26`	`+ LOCAL g`
	`27`	`+ g = gbarmh`
	`28`	`+ ik = g*(v - ek)`
`27`	`29`	`}`
`28`	`30`
`29`	`31`	`DERIVATIVE states {`