WIP

miniapp/miniapp.cpp

@@ -9,10 +9,9 @@
 
 #include <common_types.hpp>
 #include <cell.hpp>
-#include <cell_group.hpp>
 #include <communication/communicator.hpp>
 #include <communication/global_policy.hpp>
-#include <fvm_cell.hpp>
+#include <fvm_multicell.hpp>
 #include <io/exporter_spike_file.hpp>
 #include <mechanism_catalogue.hpp>
 #include <model.hpp>
@@ -29,7 +28,7 @@
 using namespace nest::mc;
 
 using global_policy = communication::global_policy;
-using lowered_cell = fvm::fvm_cell<double, cell_local_size_type>;
+using lowered_cell = fvm::fvm_multicell<double, cell_local_size_type>;
 using model_type = model<lowered_cell>;
 using time_type = model_type::time_type;
 using sample_trace_type = sample_trace<time_type, model_type::value_type>;

src/cell_group.hpp

@@ -9,7 +9,7 @@
 #include <event_queue.hpp>
 #include <spike.hpp>
 #include <spike_source.hpp>
-#include <util/singleton.hpp>
+#include <util/range.hpp>
 
 #include <profiling/profiler.hpp>
 

src/fvm_multicell.hpp

@@ -48,7 +48,7 @@ public:
 
     using detector_handle = size_type;
     using target_handle = std::pair<size_type, size_type>;
-    using probe_handle = std::pair<const vector_type fvm_cell::*, size_type>;
+    using probe_handle = std::pair<const vector_type fvm_multicell::*, size_type>;
 
     void resting_potential(value_type potential_mV) {
         resting_potential_ = potential_mV;
@@ -204,14 +204,14 @@ private:
 
     std::vector<std::pair<uint32_t, i_clamp>> stimulii_;
 
-    std::vector<std::pair<const vector_type fvm_cell::*, uint32_t>> probes_;
+    std::vector<std::pair<const vector_type fvm_multicell::*, uint32_t>> probes_;
 
     // mechanism factory
     using mechanism_catalogue = nest::mc::mechanisms::catalogue<value_type, size_type>;
 
     // perform area and capacitance calculation on initialization
     void compute_cv_area_unnormalized_capacitance(
-        std::pair<size_type, size_type> comps, const segment& seg, index_vector &parent);
+        std::pair<size_type, size_type> comps, const segment& seg, index_type &parent);
 };
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -222,7 +222,7 @@ template <typename T, typename I>
 void fvm_multicell<T, I>::compute_cv_area_unnormalized_capacitance(
     std::pair<size_type, size_type> comps,
     const segment& seg,
-    index_vector &parent)
+    index_type &parent)
 {
     using util::left;
     using util::right;
@@ -230,7 +230,7 @@ void fvm_multicell<T, I>::compute_cv_area_unnormalized_capacitance(
     // precondition: group_parent_index[j] holds the correct value for
     // j in [base_comp, base_comp+segment.num_compartments()].
 
-    if (auto soma = seg->as_soma()) {
+    if (auto soma = seg.as_soma()) {
         // confirm assumption that there is one compartment in soma
         if (comps.size()!=1)
             throw std::logic_error("soma allocated more than one compartment");
@@ -241,7 +241,7 @@ void fvm_multicell<T, I>::compute_cv_area_unnormalized_capacitance(
         cv_areas_[i] += area;
         cv_capacitance_[i] += area * soma->mechanism("membrane").get("c_m").value;
     }
-    else if (auto cable = s->as_cable()) {
+    else if (auto cable = s.as_cable()) {
         // loop over each compartment in the cable
         // each compartment has the face between two CVs at its centre
         // the centers of the CVs are the end points of the compartment
@@ -458,11 +458,7 @@ void fvm_multicell<T, I>::initialize(
         mechanisms_.push_back(std::move(mech));
     }
 
-    // TODO: FROM HERE...
-
-    /////////////////////////////////////////////
     // build the ion species
-    /////////////////////////////////////////////
     for(auto ion : mechanisms::ion_kinds()) {
         // find the compartment indexes of all compartments that have a
         // mechanism that depends on/influences ion

src/util/singleton.hpp

-#pragma once
-
-/*
- * Present a single object as a (non-owning) container with one
- * element.
- *
- * (Will be subsumed by range/view code.)
- */
-
-#include <algorithm>
-
-namespace nest {
-namespace mc {
-namespace util {
-
-template <typename X>
-struct singleton_adaptor {
-    using size_type = std::size_t;
-    using difference_type = std::ptrdiff_t;
-    using value_type = X;
-    using reference = X&;
-    using const_reference = const X&;
-    using iterator = X*;
-    using const_iterator = const X*;
-
-    X* xp;
-    singleton_adaptor(X& x): xp(&x) {}
-
-    const X* cbegin() const { return xp; }
-    const X* begin() const { return xp; }
-    X* begin() { return xp; }
-
-    const X* cend() const { return xp+1; }
-    const X* end() const { return xp+1; }
-    X* end() { return xp+1; }
-
-    std::size_t size() const { return 1u; }
-
-    bool empty() const { return false; }
-
-    const X* front() const { return *xp; }
-    X* front() { return *xp; }
-
-    const X* back() const { return *xp; }
-    X* back() { return *xp; }
-
-    const X* operator[](difference_type) const { return *xp; }
-    X* operator[](difference_type) { return *xp; }
-
-    void swap(singleton_adaptor& s) { std::swap(xp, s.xp); }
-    friend void swap(singleton_adaptor& r, singleton_adaptor& s) {
-        r.swap(s);
-    }
-};
-
-template <typename X>
-singleton_adaptor<X> singleton_view(X& x) {
-    return singleton_adaptor<X>(x);
-}
-
-} // namespace util
-} // namespace mc
-} // namespace nest

tests/unit/test_fvm.cpp

@@ -5,7 +5,7 @@
 #include <common_types.hpp>
 #include <cell.hpp>
 #include <fvm_cell.hpp>
-#include <util/singleton.hpp>
+#include <util/range.hpp>
 
 #include "../test_util.hpp"
 

tests/unit/test_probe.cpp

@@ -3,7 +3,7 @@
 #include <common_types.hpp>
 #include <cell.hpp>
 #include <fvm_cell.hpp>
-#include <util/singleton.hpp>
+#include <util/range.hpp>
 
 TEST(probe, instantiation)
 {

tests/validation/validate_ball_and_stick.cpp

@@ -4,7 +4,7 @@
 #include <common_types.hpp>
 #include <cell.hpp>
 #include <fvm_cell.hpp>
-#include <util/singleton.hpp>
+#include <util/range.hpp>
 
 #include "gtest.h"
 #include "../test_util.hpp"

tests/validation/validate_soma.cpp

@@ -4,7 +4,7 @@
 #include <common_types.hpp>
 #include <cell.hpp>
 #include <fvm_cell.hpp>
-#include <util/singleton.hpp>
+#include <util/range.hpp>
 
 #include "gtest.h"
 #include "../test_util.hpp"