fix OS X initializer list issue

.gitignore

@@ -47,3 +47,5 @@ CMakeCache.txt
 cmake_install.cmake
 Makefile
 
+# mechanism implementations generated my modparser
+include/mechanisms

src/fvm.hpp

@@ -88,6 +88,39 @@ class fvm_cell {
         return mechanisms_;
     }
 
+    /// return reference to list of ions
+    //std::map<mechanisms::ionKind, ion_type> ions_;
+    std::map<mechanisms::ionKind, ion_type>& ions() {
+        return ions_;
+    }
+    std::map<mechanisms::ionKind, ion_type> const& ions() const {
+        return ions_;
+    }
+
+    /// return reference to sodium ion
+    ion_type& ion_na() {
+        return ions_[mechanisms::ionKind::na];
+    }
+    ion_type const& ion_na() const {
+        return ions_[mechanisms::ionKind::na];
+    }
+
+    /// return reference to calcium ion
+    ion_type& ion_ca() {
+        return ions_[mechanisms::ionKind::ca];
+    }
+    ion_type const& ion_ca() const {
+        return ions_[mechanisms::ionKind::ca];
+    }
+
+    /// return reference to pottasium ion
+    ion_type& ion_k() {
+        return ions_[mechanisms::ionKind::k];
+    }
+    ion_type const& ion_k() const {
+        return ions_[mechanisms::ionKind::k];
+    }
+
     private:
 
     /// the linear system for implicit time stepping of cell state
@@ -303,6 +336,24 @@ fvm_cell<T, I>::fvm_cell(nest::mc::cell const& cell)
             }
         }
     }
+
+    // FIXME: Hard code parameters for now.
+    //        Take defaults for reversal potential of sodium and potassium from
+    //        the default values in Neuron.
+    //        We don't use the other parameters for the HH model, so I leave the NaN.
+    //        To set them I would have to go spelunking in the Neuron source.
+    using memory::all;
+    ion_ca().reversal_potential()(all)     = std::numeric_limits<value_type>::quiet_NaN();
+    ion_ca().internal_concentration()(all) = std::numeric_limits<value_type>::quiet_NaN();
+    ion_ca().external_concentration()(all) = std::numeric_limits<value_type>::quiet_NaN();
+
+    ion_na().reversal_potential()(all)     = -50.0;
+    ion_na().internal_concentration()(all) = std::numeric_limits<value_type>::quiet_NaN();
+    ion_na().external_concentration()(all) = std::numeric_limits<value_type>::quiet_NaN();
+
+    ion_k().reversal_potential()(all)     = -77.0;
+    ion_k().internal_concentration()(all) = std::numeric_limits<value_type>::quiet_NaN();
+    ion_k().external_concentration()(all) = std::numeric_limits<value_type>::quiet_NaN();
 }
 
 template <typename T, typename I>
@@ -348,7 +399,6 @@ void fvm_cell<T, I>::setup_matrix(T dt)
     }
 }
 
-
 } // namespace fvm
 } // namespace mc
 } // namespace nest

src/ion.hpp

@@ -28,15 +28,17 @@ enum class ionKind {ca, na, k};
 [[gnu::unused]] static
 std::string to_string(ionKind k)
 {
-    if(k==ionKind::na) return "sodium";
-    if(k==ionKind::ca) return "calcium";
-    if(k==ionKind::k)  return "pottasium";
-    return "unkown ion";
+    switch(k) {
+        case ionKind::na : return "sodium";
+        case ionKind::ca : return "calcium";
+        case ionKind::k  : return "pottasium";
+    }
+    return "unkown";
 }
 
 /// and a little helper to iterate over them
 [[gnu::unused]] static
-std::initializer_list<ionKind> ion_kinds()
+std::vector<ionKind> ion_kinds()
 {
     return {ionKind::ca, ionKind::na, ionKind::k};
 }

tests/test_run.cpp

@@ -9,6 +9,9 @@ TEST(run, cable)
 
     nest::mc::cell cell;
 
+    // setup global state for the mechanisms
+    nest::mc::mechanisms::setup_mechanism_helpers();
+
     cell.add_soma(6e-4); // 6um in cm
 
     // 1um radius and 4mm long, all in cm
@@ -44,6 +47,17 @@ TEST(run, cable)
     fvcell.setup_matrix(0.02);
     EXPECT_EQ(fvcell.cv_areas().size(), J.size());
 
+    // inspect ion channels
+    /*
+    std::cout << "ion na index : " << fvcell.ion_na().node_index() << "\n";
+    std::cout << "ion ca index : " << fvcell.ion_ca().node_index() << "\n";
+    std::cout << "ion k  index : " << fvcell.ion_k().node_index() << "\n";
+
+    std::cout << "ion na E : " << fvcell.ion_na().reversal_potential() << "\n";
+    std::cout << "ion ca E : " << fvcell.ion_ca().reversal_potential() << "\n";
+    std::cout << "ion k  E : " << fvcell.ion_k().reversal_potential() << "\n";
+    */
+
     //auto& cable_parms = cell.segment(1)->mechanism("membrane");
     //std::cout << soma_hh << std::endl;
     //std::cout << cable_parms << std::endl;
@@ -65,6 +79,9 @@ TEST(run, init)
 
     nest::mc::cell cell;
 
+    // setup global state for the mechanisms
+    nest::mc::mechanisms::setup_mechanism_helpers();
+
     cell.add_soma(12.6157/2.0);
     //auto& props = cell.soma()->properties;