diff --git a/arbor/fvm_layout.cpp b/arbor/fvm_layout.cpp index aa8ba5f57..e8baafef9 100644 --- a/arbor/fvm_layout.cpp +++ b/arbor/fvm_layout.cpp @@ -397,8 +397,8 @@ fvm_cv_discretize(const cable_cell& cell, // Compute auto len = embedding.integrate_length(span); for (auto& [ion, info]: diffusive_ions) { - // TODO scale to m^2/s (now at 1e-7*m^2/s) - auto sigma = len/embedding.integrate_ixa(span, info.axial_resistivity[0].at(bid)); + // TODO scale to m^2/s + auto sigma = 1e7*len/embedding.integrate_ixa(span, info.axial_resistivity[0].at(bid)); info.face_diffusivity[i] = sigma; } } diff --git a/doc/concepts/decor.rst b/doc/concepts/decor.rst index 736dcfccb..6605a91a1 100644 --- a/doc/concepts/decor.rst +++ b/doc/concepts/decor.rst @@ -231,11 +231,11 @@ can't be overridden at cell or region level. Each ion species has the following properties: -1. *internal concentration*: concentration on interior of the membrane [mM]. -2. *external concentration*: concentration on exterior of the membrane [mM]. +1. *internal concentration*: concentration on interior of the membrane :math:`[mM]`. +2. *external concentration*: concentration on exterior of the membrane :math:`[mM]`. 3. *reversal potential*: reversal potential [mV]. 4. *reversal potential mechanism*: method for calculating reversal potential. -5. *diffusivity*: diffusion coefficient for marker concentration, defaults to zero (unit is currently [10^-7 m^2/s], which will be adapted in the future). +5. *diffusivity*: diffusion coefficient for marker concentration, defaults to zero :math:`[m^2/s]`. Properties 1, 2 and 3 must be defined, and are used as the initial values for each quantity at the start of the simulation. They are specified globally, diff --git a/test/unit/test_diffusion.cpp b/test/unit/test_diffusion.cpp index 4d2f75544..ce0570122 100644 --- a/test/unit/test_diffusion.cpp +++ b/test/unit/test_diffusion.cpp @@ -150,7 +150,7 @@ TEST(diffusion, errors) { TEST(diffusion, by_initial_concentration) { auto rec = linear{30, 3, 6} - .set_diffusivity(0.005) + .set_diffusivity(5e-10) .set_concentration(0.0) .set_concentration(0.1, "(cable 0 0.5 0.6)"_reg); result_t exp = {{0.000000, 0.000000, 0.000000}, @@ -178,7 +178,7 @@ TEST(diffusion, by_initial_concentration) { TEST(diffusion, by_event) { auto rec = linear{30, 3, 6} - .set_diffusivity(0.005) + .set_diffusivity(5e-10) .set_concentration(0.0) .add_inject() .add_event(0, 0.005); @@ -235,7 +235,7 @@ TEST(diffusion, decay) { TEST(diffusion, decay_by_initial_concentration) { auto rec = linear{30, 3, 6} - .set_diffusivity(0.005) + .set_diffusivity(5e-10) .set_concentration(0.0) .set_concentration(0.1, "(cable 0 0.5 0.6)"_reg) .add_decay(); @@ -264,7 +264,7 @@ TEST(diffusion, decay_by_initial_concentration) { TEST(diffusion, decay_by_event) { auto rec = linear{30, 3, 6} - .set_diffusivity(0.005) + .set_diffusivity(5e-10) .set_concentration(0.0) .add_decay() .add_inject()