diff --git a/src/fvm_multicell.hpp b/src/fvm_multicell.hpp
index 09e55a19f6efd8a2f0859e07673f7d345f3b2383..e89ca11789e0fe644f0cb9e99cc88581258a74c0 100644
--- a/src/fvm_multicell.hpp
+++ b/src/fvm_multicell.hpp
@@ -54,6 +54,8 @@ public:
using target_handle = std::pair<size_type, size_type>;
using probe_handle = std::pair<const vector_type fvm_multicell::*, size_type>;
+ using stimulus_store_type = std::vector<std::pair<std::uint32_t, i_clamp>>;
+
void resting_potential(value_type potential_mV) {
resting_potential_ = potential_mV;
}
@@ -162,6 +164,15 @@ public:
return (v>-1000.) && (v<1000.);
}
+ /// return reference to the stimuli
+ stimulus_store_type& stimuli() {
+ return stimuli_;
+ }
+
+ stimulus_store_type const& stimuli() const {
+ return stimuli_;
+ }
+
value_type time() const { return t_; }
std::size_t num_probes() const { return probes_.size(); }
@@ -206,7 +217,7 @@ private:
/// the ion species
std::map<mechanisms::ionKind, ion_type> ions_;
- std::vector<std::pair<uint32_t, i_clamp>> stimuli_;
+ stimulus_store_type stimuli_;
std::vector<std::pair<const vector_type fvm_multicell::*, uint32_t>> probes_;
diff --git a/tests/unit/test_fvm_multi.cpp b/tests/unit/test_fvm_multi.cpp
index df8356418705c51a865a9eb1cbcbf3ce5565c90e..4592629cc7c1bf637efaf3768498b789b1693adf 100644
--- a/tests/unit/test_fvm_multi.cpp
+++ b/tests/unit/test_fvm_multi.cpp
@@ -140,3 +140,119 @@ TEST(fvm_multi, multi_init)
fvcell.setup_matrix(0.01);
}
+
+// test that stimuli are added correctly
+TEST(fvm_multi, stimulus)
+{
+ using namespace nest::mc;
+ using util::singleton_view;
+
+ // the default ball and stick has one stimulus at the terminal end of the dendrite
+ auto cell = make_cell_ball_and_stick();
+
+ // ... so add a second at the soma to make things more interesting
+ cell.add_stimulus({0,0.5}, {1., 2., 0.1});
+
+ // now we have two stims :
+ //
+ // |stim0 |stim1
+ // -----------------------
+ // delay | 5 | 1
+ // duration | 80 | 2
+ // amplitude | 0.3 | 0.1
+ // compmnt | 4 | 0
+
+
+ using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
+ std::vector<fvm_cell::target_handle> targets;
+ std::vector<fvm_cell::detector_handle> detectors;
+ std::vector<fvm_cell::probe_handle> probes;
+
+ fvm_cell fvcell;
+ fvcell.initialize(singleton_view(cell), detectors, targets, probes);
+
+ auto& stim = fvcell.stimuli();
+ EXPECT_EQ(stim.size(), 2u);
+
+ EXPECT_EQ(stim[0].first, 4u);
+ EXPECT_EQ(stim[1].first, 0u);
+
+ EXPECT_EQ(stim[0].second.delay(), 5.);
+ EXPECT_EQ(stim[1].second.delay(), 1.);
+ EXPECT_EQ(stim[0].second.duration(), 80.);
+ EXPECT_EQ(stim[1].second.duration(), 2.);
+ EXPECT_EQ(stim[0].second.amplitude(), 0.3);
+ EXPECT_EQ(stim[1].second.amplitude(), 0.1);
+}
+
+// test that mechanism indexes are computed correctly
+TEST(fvm_multi, mechanism_indexes)
+{
+ using namespace nest::mc;
+
+ // create a cell with 4 sements:
+ // a soma with a branching dendrite
+ // - hh on soma and first branch of dendrite (segs 0 and 2)
+ // - pas on main dendrite and second branch (segs 1 and 3)
+ //
+ // /
+ // pas
+ // /
+ // hh---pas--.
+ // \.
+ // hh
+ // \.
+
+ cell c;
+ auto soma = c.add_soma(12.6157/2.0);
+ soma->add_mechanism(hh_parameters());
+
+ // add dendrite of length 200 um and diameter 1 um with passive channel
+ c.add_cable(0, segmentKind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(1, segmentKind::dendrite, 0.5, 0.5, 100);
+ c.add_cable(1, segmentKind::dendrite, 0.5, 0.5, 100);
+
+ auto& segs = c.segments();
+ segs[1]->add_mechanism(pas_parameters());
+ segs[2]->add_mechanism(hh_parameters());
+ segs[3]->add_mechanism(pas_parameters());
+
+ for (auto& seg: segs) {
+ if (seg->is_dendrite()) {
+ seg->mechanism("membrane").set("r_L", 100);
+ seg->set_compartments(4);
+ }
+ }
+
+ // generate the lowered fvm cell
+ using fvm_cell = fvm::fvm_multicell<double, cell_lid_type>;
+ std::vector<fvm_cell::target_handle> targets;
+ std::vector<fvm_cell::detector_handle> detectors;
+ std::vector<fvm_cell::probe_handle> probes;
+
+ fvm_cell fvcell;
+ fvcell.initialize(util::singleton_view(c), detectors, targets, probes);
+
+ // make vectors with the expected CV indexes for each mechanism
+ std::vector<unsigned> hh_index = {0u, 4u, 5u, 6u, 7u, 8u};
+ std::vector<unsigned> pas_index = {0u, 1u, 2u, 3u, 4u, 9u, 10u, 11u, 12u};
+ // iterate over mechanisms and test whether they were assigned to the correct CVs
+ // TODO : this fails because we do not handle CVs at branching points (including soma) correctly
+ for(auto& mech : fvcell.mechanisms()) {
+ auto const& ni = mech->node_index();
+ if(mech->name()=="hh") {
+ EXPECT_EQ(ni.size(), hh_index.size());
+ // only check index by index if size of index arrays match
+ if(ni.size()==hh_index.size()) {
+ for(auto i : util::make_span(0u, ni.size())) EXPECT_EQ(ni[i], hh_index[i]);
+ }
+ }
+ else if(mech->name()=="pas") {
+ EXPECT_EQ(ni.size(), pas_index.size());
+ // only check index by index if size of index arrays match
+ if(ni.size()==pas_index.size()) {
+ for(auto i : util::make_span(0u, ni.size())) EXPECT_EQ(ni[i], pas_index[i]);
+ }
+ }
+ }
+}