Adjust tests.

arbor-sim · Jan 13, 2024 · 00ac312 · 00ac312
1 parent 10a492d
commit 00ac312
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Showing 7 changed files with 19 additions and 17 deletions.
diff --git a/arbor/include/arbor/cable_cell_param.hpp b/arbor/include/arbor/cable_cell_param.hpp
@@ -139,7 +139,7 @@ struct ARB_SYMBOL_VISIBLE init_membrane_potential {
     init_membrane_potential() = default;
     init_membrane_potential(const U::quantity& m, iexpr scale=1):
       value(m.value_as(U::mV)), scale{scale} {
-        if (!std::isnan(value)) throw std::domain_error{"Value must be finite and in [mV]."};
+        if (std::isnan(value)) throw std::domain_error{"Value must be finite and in [mV]."};
     }
 };
 
@@ -461,13 +461,13 @@ struct ARB_SYMBOL_VISIBLE cable_cell_global_properties {
 
         auto &ion_data = default_parameters.ion_data[ion_name];
         ion_data.init_int_concentration = init_iconc.value_as(U::mM);
-        if (std::isnan(*ion_data.init_int_concentration)) throw cable_cell_error("init_int_concentration must be finite and convertible to mM");
+        if (std::isnan(*ion_data.init_int_concentration)) throw std::domain_error("init_int_concentration must be finite and convertible to mM");
         ion_data.init_ext_concentration = init_econc.value_as(U::mM);
-        if (std::isnan(*ion_data.init_ext_concentration)) throw cable_cell_error("init_ext_concentration must be finite and convertible to mM");
+        if (std::isnan(*ion_data.init_ext_concentration)) throw std::domain_error("init_ext_concentration must be finite and convertible to mM");
         ion_data.init_reversal_potential = init_revpot.value_as(U::mV);
-        if (std::isnan(*ion_data.init_reversal_potential)) throw cable_cell_error("init_reversal_potential must be finite and convertible to mV");
+        if (std::isnan(*ion_data.init_reversal_potential)) throw std::domain_error("init_reversal_potential must be finite and convertible to mV");
         ion_data.diffusivity = diffusivity.value_as(U::m2/U::s);
-        if (std::isnan(*ion_data.diffusivity) || *ion_data.diffusivity < 0) throw cable_cell_error("diffusivity must be positive, finite, and convertible to m2/s");
+        if (std::isnan(*ion_data.diffusivity) || *ion_data.diffusivity < 0) throw std::domain_error("diffusivity must be positive, finite, and convertible to m2/s");
     }
 
     void add_ion(const std::string& ion_name,

diff --git a/example/diffusion/diffusion.cpp b/example/diffusion/diffusion.cpp
@@ -27,7 +27,7 @@ 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, b);
+        gprop.add_ion("bla", 1, 23*U::mM, 42*U::mM, 0*U::mV, b*U::m2/U::s);
     }
 
     cell_size_type num_cells()                                   const override { return 1; }

diff --git a/test/simple_recipes.hpp b/test/simple_recipes.hpp
@@ -10,13 +10,14 @@
 #include <arbor/cable_cell.hpp>
 #include <arbor/cable_cell_param.hpp>
 #include <arbor/recipe.hpp>
+#include <arbor/units.hpp>
 #include <arbor/util/unique_any.hpp>
 
 
-#include "util/rangeutil.hpp"
-
 namespace arb {
 
+namespace U = units;
+
 // Common functionality: maintain an unordered map of probe data
 // per gid, built with `add_probe()`.
 
@@ -48,7 +49,7 @@ class simple_recipe_base: public recipe {
     }
 
     void add_ion(const std::string& ion_name, int charge, double init_iconc, double init_econc, double init_revpot) {
-        cell_gprop_.add_ion(ion_name, charge, init_iconc, init_econc, init_revpot);
+        cell_gprop_.add_ion(ion_name, charge, init_iconc*U::mM, init_econc*U::mM, init_revpot*U::mV);
     }
 
     void nernst_ion(const std::string& ion_name) {

diff --git a/test/unit/test_diffusion.cpp b/test/unit/test_diffusion.cpp
@@ -315,27 +315,27 @@ TEST(diffusion, setting_diffusivity) {
     // BAD: Trying to use a diffusive ion, but b=0.
     {
         R r;
-        r.gprop.add_ion("bla", 1, 23, 42, 0, 0);
+        r.gprop.add_ion("bla", 1, 23*U::mM, 42*U::mM, 0*U::mV, 0*U::m2/U::s);
         EXPECT_THROW(simulation(r).run(1*arb::units::ms, 1*arb::units::ms), illegal_diffusive_mechanism);
     }
     // BAD: Trying to use a partially diffusive ion
     {
         R r;
-        r.gprop.add_ion("bla", 1, 23, 42, 0, 0);
+        r.gprop.add_ion("bla", 1, 23*U::mM, 42*U::mM, 0*U::mV, 0*U::m2/U::s);
         r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13*U::m.pow(2)/U::s});
         EXPECT_THROW(simulation(r).run(1*arb::units::ms, 1*arb::units::ms), cable_cell_error);
     }
     // OK: Using the global default
     {
         R r;
-        r.gprop.add_ion("bla", 1, 23, 42, 0, 8);
+        r.gprop.add_ion("bla", 1, 23*U::mM, 42*U::mM, 0*U::mV, 8*U::m2/U::s);
         r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13*U::m.pow(2)/U::s});
         EXPECT_NO_THROW(simulation(r).run(1*arb::units::ms, 1*arb::units::ms));
     }
     // OK: Using the cell default
     {
         R r;
-        r.gprop.add_ion("bla", 1, 23, 42, 0, 0);
+        r.gprop.add_ion("bla", 1, 23*U::mM, 42*U::mM, 0*U::mV, 0*U::m2/U::s);
         r.dec.set_default(ion_diffusivity{"bla", 8*U::m.pow(2)/U::s});
         r.dec.paint("(tag 1)"_reg, ion_diffusivity{"bla", 13*U::m.pow(2)/U::s});
         EXPECT_NO_THROW(simulation(r).run(1*arb::units::ms, 1*arb::units::ms));

diff --git a/test/unit/test_fvm_layout.cpp b/test/unit/test_fvm_layout.cpp
@@ -1626,9 +1626,9 @@ TEST(fvm_layout, revpot) {
     gprop.catalogue = make_unit_test_catalogue();
 
     gprop.ion_species = {{"a", 1}, {"b", 2}, {"c", 3}};
-    gprop.add_ion("a", 1, 10., 0, 0);
-    gprop.add_ion("b", 2, 30., 0, 0);
-    gprop.add_ion("c", 3, 50., 0, 0);
+    gprop.add_ion("a", 1, 10.*U::mM, 0*U::mM, 0*U::mV);
+    gprop.add_ion("b", 2, 30.*U::mM, 0*U::mM, 0*U::mV);
+    gprop.add_ion("c", 3, 50.*U::mM, 0*U::mM, 0*U::mV);
 
     gprop.default_parameters.reversal_potential_method["a"] = "write_eX/a";
     mechanism_desc write_eb_ec = "write_multiple_eX/x=b,y=c";

diff --git a/test/unit/test_fvm_lowered.cpp b/test/unit/test_fvm_lowered.cpp
@@ -33,6 +33,7 @@
 #include "../common_cells.hpp"
 #include "../simple_recipes.hpp"
 
+
 using namespace std::string_literals;
 using namespace arborio::literals;
 

diff --git a/test/unit/test_recipe.cpp b/test/unit/test_recipe.cpp
@@ -62,7 +62,7 @@ cable_cell custom_cell(cell_size_type num_detectors, cell_size_type num_synapses
     // Add a num_detectors detectors to the cell.
     for (auto i: util::make_span(num_detectors)) {
         decorations.place(arb::mlocation{0,(double)i/num_detectors},
-                          arb::threshold_detector{10*arb::units::ms}, "detector"+std::to_string(i));
+                          arb::threshold_detector{10*arb::units::mV}, "detector"+std::to_string(i));
     }
 
     // Add a num_synapses synapses to the cell.