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Adjust Diffusion Scaling #2439

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Adjust Diffusion Scaling #2439

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e86a368
Adjust scaling.
thorstenhater Jan 22, 2025
f00b366
fix scaling
thorstenhater Jan 22, 2025
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4 changes: 2 additions & 2 deletions arbor/fvm_layout.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
}
}
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6 changes: 3 additions & 3 deletions doc/concepts/decor.rst
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Expand Up @@ -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,
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8 changes: 4 additions & 4 deletions test/unit/test_diffusion.cpp
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Expand Up @@ -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},
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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()
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