Bugfix: hh_soma.jl

* Use consistent scaling for y[1] scalar voltage in hh_soma.jl
* Also: add more reserved target names to CMakeLists.txt
  helper function.

validation/CMakeLists.txt

@@ -5,12 +5,14 @@ add_custom_target(validation_data)
 # Helper function because ffs CMake.
 
 function(make_unique_target_name name path)
-    # try and make a broadly human readable target name if possible.
+    # Try and make a broadly human readable target name if possible.
     string(REGEX REPLACE ".*/" "" leaf "${path}")
     string(REGEX REPLACE "[^a-zA-Z0-9_.+-]" "_" canon "${leaf}")
 
-    # check against reserved names, of which of course there is no documented list
-    if(canon MATCHES "^(all|test|clean|help)$")
+    # Check against reserved names, of which of course there is no documented list
+    # except in the sodding CMake source code. Seriously. Look at the CMP0037 policy
+    # text for a laugh.
+    if(canon MATCHES "^(all|ALL_BUILD|help|install|INSTALL|preinstall|clean|edit_cache|rebuild_cache|test|RUN_TESTS|package|PACKAGE|package_source|ZERO_CHECK)$")
         set(canon "${canon}_")
     endif()
     while((TARGET "${canon}"))

validation/ref/numeric/hh_soma.jl

@@ -62,11 +62,16 @@ function n_lims(v)
     return ntau, ninf
 end
 
-# v = y[1]
+# v = y[1] V
 # m = y[2]
 # h = y[3]
 # n = y[4]
 
+# dv/dt = ydot[1] V/s
+# dm/dt = ydot[2] /s
+# dh/dt = ydot[3] /s
+# dn/dt = ydot[4] /s
+
 # choose initial conditions for the system such that the gating variables
 # are at steady state for the user-specified voltage v
 function initial_conditions(v)
@@ -74,13 +79,13 @@ function initial_conditions(v)
     htau, hinf = h_lims(v)
     ntau, ninf = n_lims(v)
 
-    return [Float64(v), minf, hinf, ninf]
+    return [v/V, minf, hinf, ninf]
 end
 
 # calculate the lhs of the ODE system
 function f(t, y, ydot)
     # copy variables into helper variable
-    v = y[1]mV
+    v = y[1]V
     m, h, n = y[2], y[3], y[4]
 
     # calculate current due to ion channels
@@ -94,7 +99,8 @@ function f(t, y, ydot)
     # calculate current due to stimulus
     #c.add_stimulus({0,0.5}, {10., 100., 0.1});
     ielectrode = 0.0nA / surface_area
-    if t>=Float64(10ms) && t<Float64(100ms)
+    time = t*ms
+    if time>=10ms && time<100ms
         ielectrode = 0.1nA / surface_area
     end
 
@@ -107,11 +113,11 @@ function f(t, y, ydot)
     htau, hinf = h_lims(v)
 
     # set the derivatives
-    # note tha these are in SI units, which are indicated in comments
-    ydot[1] = Float64(i/c_m)            # V*s^-1
-    ydot[2] = Float64((minf-m)/mtau)    # s^-1
-    ydot[3] = Float64((hinf-h)/htau)    # s^-1
-    ydot[4] = Float64((ninf-n)/ntau)    # s^-1
+    # note values are in SI units, as determined by the scaling factors:
+    ydot[1] = i/c_m         / (V/s)
+    ydot[2] = (minf-m)/mtau / (1/s)
+    ydot[3] = (hinf-h)/htau / (1/s)
+    ydot[4] = (ninf-n)/ntau / (1/s)
 
     return Sundials.CV_SUCCESS
 end