From 0a4f0c3b1725f5538ade6ec27f6819ed9a970ae7 Mon Sep 17 00:00:00 2001
From: Ben Cumming <bcumming@cscs.ch>
Date: Mon, 2 May 2016 09:32:14 +0200
Subject: [PATCH] fix OS X initializer list issue
---
.gitignore | 2 ++
src/fvm.hpp | 52 +++++++++++++++++++++++++++++++++++++++++++++-
src/ion.hpp | 12 ++++++-----
tests/test_run.cpp | 17 +++++++++++++++
4 files changed, 77 insertions(+), 6 deletions(-)
diff --git a/.gitignore b/.gitignore
index c23dfde0..cd1f0915 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,3 +47,5 @@ CMakeCache.txt
cmake_install.cmake
Makefile
+# mechanism implementations generated my modparser
+include/mechanisms
diff --git a/src/fvm.hpp b/src/fvm.hpp
index c6c458c7..674c7d0e 100644
--- a/src/fvm.hpp
+++ b/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
diff --git a/src/ion.hpp b/src/ion.hpp
index 2f780616..311e8600 100644
--- a/src/ion.hpp
+++ b/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};
}
diff --git a/tests/test_run.cpp b/tests/test_run.cpp
index 55c9c6fc..55fb0d0f 100644
--- a/tests/test_run.cpp
+++ b/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;
--
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