diff --git a/src/cell.cpp b/src/cell.cpp
index e96cae69aca834d61d81c9c53c9488532a3b5b69..f247a2a8a83e327abce312ca31b31c5e560b8ce6 100644
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -188,7 +188,7 @@ void cell::add_stimulus(segment_location loc, i_clamp stim)
)
);
}
- stimulii_.push_back({loc, std::move(stim)});
+ stimuli_.push_back({loc, std::move(stim)});
}
void cell::add_detector(segment_location loc, double threshold)
diff --git a/src/cell.hpp b/src/cell.hpp
index 746549289f1b718433388e92f5f1ca9d13d433c1..bd83b1b182238377cdd9e7642c60d0be31fe4892 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -129,18 +129,18 @@ public:
compartment_model model() const;
//////////////////
- // stimulii
+ // stimuli
//////////////////
void add_stimulus(segment_location loc, i_clamp stim);
std::vector<stimulus_instance>&
- stimulii() {
- return stimulii_;
+ stimuli() {
+ return stimuli_;
}
const std::vector<stimulus_instance>&
- stimulii() const {
- return stimulii_;
+ stimuli() const {
+ return stimuli_;
}
//////////////////
@@ -188,8 +188,8 @@ private:
// the segments
std::vector<segment_ptr> segments_;
- // the stimulii
- std::vector<stimulus_instance> stimulii_;
+ // the stimuli
+ std::vector<stimulus_instance> stimuli_;
// the synapses
std::vector<synapse_instance> synapses_;
diff --git a/src/fvm_cell.hpp b/src/fvm_cell.hpp
index 83fd8b769974f8447b3930d8f2477a0732d139fe..1d9ff96568dc3c2817944145330e9a7178c19e05 100644
--- a/src/fvm_cell.hpp
+++ b/src/fvm_cell.hpp
@@ -288,7 +288,7 @@ private:
/// the ion species
std::map<mechanisms::ionKind, ion_type> ions_;
- std::vector<std::pair<uint32_t, i_clamp>> stimulii_;
+ std::vector<std::pair<uint32_t, i_clamp>> stimuli_;
std::vector<std::pair<const vector_type fvm_cell::*, uint32_t>> probes_;
@@ -531,10 +531,10 @@ void fvm_cell<T, I>::initialize(
ion_ca().internal_concentration()(all) = 5e-5; // mM
ion_ca().external_concentration()(all) = 2.0; // mM
- // add the stimulii
- for(const auto& stim : cell.stimulii()) {
+ // add the stimuli
+ for(const auto& stim : cell.stimuli()) {
auto idx = find_compartment_index(stim.location, graph);
- stimulii_.push_back( {idx, stim.clamp} );
+ stimuli_.push_back( {idx, stim.clamp} );
}
// record probe locations by index into corresponding state vector
@@ -633,8 +633,8 @@ void fvm_cell<T, I>::advance(T dt) {
PL();
}
- // add current contributions from stimulii
- for (auto& stim : stimulii_) {
+ // add current contributions from stimuli
+ for (auto& stim : stimuli_) {
auto ie = stim.second.amplitude(t_); // [nA]
auto loc = stim.first;
diff --git a/src/fvm_multicell.hpp b/src/fvm_multicell.hpp
index 709273adfac72a0f485162318757703f51d9a522..be7a5e322b380d703b53315ad1d30a570b0245e8 100644
--- a/src/fvm_multicell.hpp
+++ b/src/fvm_multicell.hpp
@@ -300,9 +300,12 @@ void fvm_multicell<T, I>::initialize(
using util::size;
// count total detectors, targets and probes for validation of handle container sizes
- size_type detectors_total = 0u;
- size_type targets_total = 0u;
- size_type probess_total = 0u;
+ size_type detectors_count = 0u;
+ size_type targets_count = 0u;
+ size_type probess_count = 0u;
+ size_type detectors_size = util::size(detector_handles);
+ size_type targets_size = util::size(targets_handles);
+ size_type probes_size = util::size(probes_handles);
auto ncell = util::size(cells);
auto cell_num_compartments =
@@ -327,7 +330,11 @@ void fvm_multicell<T, I>::initialize(
// initialize vector used for matrix creation.
index_vector group_parent_index{ncomp, 0};
+ // create each cell:
auto target_hi = target_handles.begin();
+ auto detector_hi = detector_handles.begin();
+ auto probe_hi = probe_handles.begin();
+
for (size_type i = 0; i<ncell; ++i) {
const auto& c = cells[i];
auto comps = cell_comp_part[i];
@@ -359,6 +366,8 @@ void fvm_multicell<T, I>::initialize(
}
for (const auto& syn: c.synapses()) {
+ EXPECTS(targets_count < targets_size);
+
const auto& name = syn.mechanism.name();
std::size_t index = 0;
if (syn_mech_indices.count(name)==0) {
@@ -371,12 +380,10 @@ void fvm_multicell<T, I>::initialize(
}
size_type syn_comp = comps.first+find_compartment_index(syn.location, graph);
+ syn_mech_map[index].push_back(syn_comp);
- EXPECTS(targets_total < c.targets.size());
*target_hi++ = target_handle{index, syn_mech_map[index].size()};
- ++targets_total;
-
- syn_mech_map[index].push_back(syn_comp);
+ ++targets_count;
}
// normalize capacitance across cell
@@ -384,14 +391,44 @@ void fvm_multicell<T, I>::initialize(
cv_capacitance_[k] /= cv_areas_[k];
}
- detectors_total += c.detectors().size();
- probess_total += c.probes.size();
+ // add the stimulii
+ for (const auto& stim: c.stimuli()) {
+ auto idx = comps.first+find_compartment_index(stim.location, graph);
+ stimuli_.push_back({idx, stim.clamp});
+ }
+
+ // detector handles are just their corresponding compartment indices
+ for (const auto& detector: c.detectors()) {
+ EXPECTS(detectors_count < detectors_size);
+
+ auto comp = comps.first+find_compartment_index(detector.location, graph);
+ *detector_hi++ = comp;
+ ++detectors_count;
+ }
+
+ // record probe locations by index into corresponding state vector
+ for (const auto& probe: c.probes()) {
+ EXPECTS(probes_count < probes_size);
+
+ auto comp = comps.first+find_compartment_index(probe.location, graph);
+ switch (probe.kind) {
+ case probeKind::membrane_voltage:
+ *probe_hi++ = {&fvm_multicell::voltage_, comp};
+ break;
+ case probeKind::membrane_current:
+ *probe_hi++ = {&fvm_multicell::current_, comp};
+ break;
+ default:
+ throw std::logic_error("unrecognized probeKind");
+ }
+ ++probes_count;
+ }
}
// confirm write-parameters were appropriately sized
- EXPECTS(util::size(detector_handles)==detectors_total);
- EXPECTS(util::size(target_handles)==targets_total);
- EXPECTS(util::size(probe_handles)==probes_total);
+ EXPECTS(detectors_size==detectors_count);
+ EXPECTS(targets_size==targets_count);
+ EXPECTS(probes_size==probes_count);
// initalize matrix
matrix_ = matrix_type(group_parent_index);
@@ -473,42 +510,12 @@ void fvm_multicell<T, I>::initialize(
ion_ca().internal_concentration()(all) = 5e-5; // mM
ion_ca().external_concentration()(all) = 2.0; // mM
- // add the stimulii
- for(const auto& stim : cell.stimulii()) {
- auto idx = find_compartment_index(stim.location, graph);
- stimulii_.push_back( {idx, stim.clamp} );
- }
-
- // record probe locations by index into corresponding state vector
- auto probe_hi = probe_handles.begin();
- for (auto probe : cell.probes()) {
- auto comp = find_compartment_index(probe.location, graph);
- switch (probe.kind) {
- case probeKind::membrane_voltage:
- *probe_hi = {&fvm_cell::voltage_, comp};
- break;
- case probeKind::membrane_current:
- *probe_hi = {&fvm_cell::current_, comp};
- break;
- default:
- throw std::logic_error("unrecognized probeKind");
- }
- ++probe_hi;
- }
-
- // detector handles are just their corresponding compartment indices
- auto detector_hi = detector_handles.begin();
- for (auto detector : cell.detectors()) {
- auto comp = find_compartment_index(detector.location, graph);
- *detector_hi++ = comp;
- }
-
// initialise mechanism and voltage state
reset();
}
template <typename T, typename I>
-void fvm_cell<T, I>::setup_matrix(T dt) {
+void fvm_multicell<T, I>::setup_matrix(T dt) {
using memory::all;
// convenience accesors to matrix storage
@@ -552,7 +559,7 @@ void fvm_cell<T, I>::setup_matrix(T dt) {
}
template <typename T, typename I>
-void fvm_cell<T, I>::reset() {
+void fvm_multicell<T, I>::reset() {
voltage_(memory::all) = resting_potential_;
t_ = 0.;
for (auto& m : mechanisms_) {
@@ -561,7 +568,7 @@ void fvm_cell<T, I>::reset() {
}
template <typename T, typename I>
-void fvm_cell<T, I>::advance(T dt) {
+void fvm_multicell<T, I>::advance(T dt) {
using memory::all;
PE("current");