`Region Reunification (gvec)`

Module: tutorials.02_EP_tissue.05D_Region_Reunification.run

Section author: Patrick Boyle <pmjboyle@gmail.com>

This tutorial details how to output the values of state variables over time during a simulation using the gvec[] interface. This tutorial is a stub to demonstrate the most basic functionality and should be expanded when possible.

Problem Setup

This example will run one simulation using a 2D sheet model (1 cm x 1 cm) that has been divided into four regions, each of which uses a different ionic model. All four models have an implementation of the fast sodium current ( $I_{Na}$ ), but in one of the models the state variable names are upper-case instead of lower-case (i.e., $M/H/J$ vs. $m/h/j$ ). The gvec[] interface is used to reunify these state variables from the four regions and output three IGB files: I_Na_m.igb, I_Na_h.igb, and I_Na_j.igb.

Usage

No optional arguments are available.

If the program is run with the --visualize option, meshalyzer will automatically load the produced I_Na_m.igb file, which shows $I_{Na}(t)$ for the entire simulation domain.

What’s Going On Under The Hood?

The relevant part of the .par file for this example is shown below:

#############################################################
num_gvecs                = 3
#############################################################
gvec[0].name             = INa_m
gvec[0].ID[0]            = m
gvec[0].ID[1]            = m
gvec[0].ID[2]            = M # <== Note upper-case letter
gvec[0].ID[3]            = m

gvec[1].name             = INa_h
gvec[1].ID[0]            = h
gvec[1].ID[1]            = h
gvec[1].ID[2]            = H # <== Note upper-case letter
gvec[1].ID[3]            = h

gvec[2].name             = INa_j
gvec[2].ID[0]            = j
gvec[2].ID[1]            = j
gvec[2].ID[2]            = J # <== Note upper-case letter
gvec[2].ID[3]            = j

Each gvec[] structure contains information about one variable that is to be reunified and output. Note that unlike gregion[] and imp_region[], there are no .num_ID variables here. That is because the number of entries in each .ID array is actually determined by num_imp_regions. In this example, the relevant imp_region details are as follows:

imp_region[0].im = converted_LRDII_F
imp_region[0].im = converted_RNC
imp_region[0].im = converted_TT2
imp_region[0].im = converted_UCLA_RAB

As noted above, state variables associated with the fast sodium current are $M/H/J$ in the TT2 implementation vs. $m/h/j$ in the other 3. This is why the gvec[].ID[2] entries, which are linked to TT2 in imp_region[2], are upper-case instead of lower-case.