diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp
index 27d59688c706ee05a87431e0fbda478228c90eb2..94a8e1071f2e8c4f3eacd5089975aea4a3d2fb35 100644
--- a/arbor/fvm_layout.cpp
+++ b/arbor/fvm_layout.cpp
@@ -16,8 +16,6 @@
#include <arbor/morph/mprovider.hpp>
#include <arbor/morph/morphology.hpp>
-#include <iostream>
-
#include "fvm_layout.hpp"
#include "threading/threading.hpp"
#include "util/maputil.hpp"
@@ -315,11 +313,18 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
id_map.insert(k, 1.0/v.value);
}
}
- // Fetch defaults, either global or per cell
- auto gd = *(value_by_key(dflt.ion_data, ion).value().diffusivity
- | value_by_key(global_dflt.ion_data, ion).value().diffusivity);
- if (gd <= 0.0) {
- throw cable_cell_error{util::pprintf("Illegal global diffusivity '{}' for ion '{}'.", gd, ion)};
+ arb_value_type def = 0.0;
+ if (auto data = value_by_key(global_dflt.ion_data, ion);
+ data && data->diffusivity) {
+ def = data->diffusivity.value();
+ }
+ if (auto data = value_by_key(dflt.ion_data, ion);
+ data && data->diffusivity) {
+ def = data->diffusivity.value();
+ }
+ if (def <= 0.0) {
+ throw cable_cell_error{util::pprintf("Illegal global diffusivity '{}' for ion '{}'; possibly unset."
+ " Please define a positive global or cell default.", def, ion)};
}
// Write inverse diffusivity / diffuse resistivity map
@@ -328,7 +333,7 @@ ARB_ARBOR_API fvm_cv_discretization fvm_cv_discretize(const cable_cell& cell, co
msize_t n_branch = D.geometry.n_branch(0);
id.reserve(n_branch);
for (msize_t i = 0; i<n_branch; ++i) {
- auto pw = pw_over_cable(id_map, mcable{i, 0., 1.}, 1.0/gd);
+ auto pw = pw_over_cable(id_map, mcable{i, 0., 1.}, 1.0/def);
id[0].push_back(pw);
}
// Prepare conductivity map
diff --git a/example/diffusion/diffusion.cpp b/example/diffusion/diffusion.cpp
index 6b0bb382ec0e4da5f5311542c0c10459c987e930..4a1454baba7b2c22a4b11528a0ac0b4fbf7d42fa 100644
--- a/example/diffusion/diffusion.cpp
+++ b/example/diffusion/diffusion.cpp
@@ -25,6 +25,7 @@ struct linear: public recipe {
linear(double ext, double dx, double Xi, double beta): l{ext}, d{dx}, i{Xi}, b{beta} {
gprop.default_parameters = neuron_parameter_defaults;
gprop.default_parameters.discretization = cv_policy_max_extent{d};
+ gprop.add_ion("bla", 1, 23, 42, 0, 0);
}
cell_size_type num_cells() const override { return 1; }
@@ -37,12 +38,13 @@ struct linear: public recipe {
// -----|-----
segment_tree tree;
tree.append(mnpos, { -l, 0, 0, 3}, {l, 0, 0, 3}, 1);
+ tree.append(0, { -l, 0, 0, 3}, {l, 0, 0, 3}, 2);
// Setup
decor decor;
decor.set_default(init_int_concentration{"na", i});
- decor.set_default(ion_diffusivity{"na", b});
- decor.place("(location 0 0.5)"_ls, synapse("inject/x=na", {{"alpha", 200.0*l}}), "Zap");
- decor.paint("(all)"_reg, density("decay/x=na"));
+ decor.paint("(tag 1)"_reg, ion_diffusivity{"na", b});
+ decor.place("(location 0 0.5)"_ls, synapse("inject/x=bla", {{"alpha", 200.0*l}}), "Zap");
+ decor.paint("(all)"_reg, density("decay/x=bla"));
return cable_cell({tree}, decor);
}
diff --git a/test/unit/test_diffusion.cpp b/test/unit/test_diffusion.cpp
index de56e11aa0c8235117e94b8cbdb7877b46656a22..aa0e07b48334c78044b8bef7be3f2928667d90e7 100644
--- a/test/unit/test_diffusion.cpp
+++ b/test/unit/test_diffusion.cpp
@@ -288,3 +288,64 @@ TEST(diffusion, decay_by_event) {
{ 0.100000, 0.900000, 0.000000}};
EXPECT_TRUE(run(rec, exp));
}
+
+TEST(diffusion, setting_diffusivity) {
+ // Skeleton recipe
+ struct R: public recipe {
+ R() {
+ gprop.default_parameters = neuron_parameter_defaults;
+ // make a two region tree
+ tree.append(mnpos, { -1, 0, 0, 3}, {1, 0, 0, 3}, 1);
+ tree.append(0, { -1, 0, 0, 3}, {1, 0, 0, 3}, 2);
+ // Utilise diffusive ions
+ dec.place("(location 0 0.5)"_ls, synapse("inject/x=bla", {{"alpha", 200.0}}), "Zap");
+ dec.paint("(all)"_reg, density("decay/x=bla"));
+ }
+
+ cell_size_type num_cells() const override { return 1; }
+ cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
+ std::any get_global_properties(cell_kind) const override { return gprop; }
+ util::unique_any get_cell_description(cell_gid_type) const override { return cable_cell({tree}, dec); }
+
+ cable_cell_global_properties gprop;
+ segment_tree tree;
+ decor dec;
+ };
+
+ // BAD: Trying to use a diffusive ion, but b=0.
+ {
+ R r;
+ r.gprop.add_ion("bla", 1, 23, 42, 0, 0);
+ EXPECT_THROW(simulation(r).run(1, 1), illegal_diffusive_mechanism);
+ }
+ // BAD: Trying to use a partially diffusive ion
+ {
+ R r;
+ r.gprop.add_ion("bla", 1, 23, 42, 0, 0);
+ r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13});
+ EXPECT_THROW(simulation(r).run(1, 1), cable_cell_error);
+ }
+ // OK: Using the global default
+ {
+ R r;
+ r.gprop.add_ion("bla", 1, 23, 42, 0, 8);
+ r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13});
+ EXPECT_NO_THROW(simulation(r).run(1, 1));
+ }
+ // OK: Using the cell default
+ {
+ R r;
+ r.gprop.add_ion("bla", 1, 23, 42, 0, 0);
+ r.dec.set_default(ion_diffusivity{"bla", 8});
+ r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13});
+ EXPECT_NO_THROW(simulation(r).run(1, 1));
+ }
+ // BAD: Using an unknown species
+ {
+ R r;
+ r.dec.set_default(ion_diffusivity{"bla", 8});
+ r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13});
+ EXPECT_THROW(simulation(r).run(1, 1), cable_cell_error);
+ }
+
+}