Run Instructions

I will use ':>' to denote running a (bash) script from terminal and '>>' to denote running a matlab program (in matlab command line). Here are the steps:

Executing a single run (time depenents PDE)

1. If initParams is not in working dir, run copy parameters: cpParams. Parameters can be in physical or scaled units, but be consistent!

    >> cpParams

or

    :> ./cpParams

2. Edit parameters in initParams. And save

3. Run the code:

• Run it in MATLAB

>> runHydrogel

• Or submit a local job

:> ./submitHgLocal

• Or submit a job to a cluster (slurm). This may need to be edited as mine is currently set-up to run on CU biogrontiers cluster fiji

:> sbatch --jobname=a_job_name fijiSlurmRunHydrogel.pbs

4. Outputs placed in a directory in ./runfiles

Calculating selectivity (PDE/ODE)

Example runs are included in the comments of fluxODE, fluxPDE, fluxParamIn

Calculating paper results

There are two wrappers that generate the data (calls fluxODE/fluxPDE/fluxODEParamIn) and make the plots (calls plot routines) for the paper. Each result has it's own paramInput file located in ./paperInits. Both functions require a vector input denotating which results/plots to want to generate and make. See the comments for more info. To make the results with key value 1, 2, 3:

>> paperResultsMaker([1:3])

Then to make the corresponding plots

>> paperPlotMaker([1:3])

On fiji

Make sure there is a file called 'initPaperResults' that has a variable with the runs you want. This file will not be tracked.

:> sbatch --jobname=a_job_name fijiSlurmPaerResults.sh

WD Function Description

initParams.m: (parameter file) Set parameters for runHydrogel, fluxPDE, fluxODE

runHydrogel.m: (executeable) runs temporal evolution of PDE.

fluxODE.m: (function) finds the flux at steady state using and ODE solver. Uses initParams.

fluxPDE.m: (function) finds flux at steady state, slope dj/dt at half max flux, and time till half max slope by solving PDE. Uses initParams.

fluxODEParamIN.m: (function) finds the flux at steady state using and ODE solver. Uses initParams and parameter inputs

cpParams.m: (executeable) copies master parameter file to initParams in WD

cleanme.m: (executeable) destroys all txt, fig, jpg, avi files in WD

nonDimParamCalc.m: (function) calculate scaled parameters from physical parameters

paperPlotMaker.m: (function) generate figures for the paper

paperResultsMaker.m: (function) generate figures for the paper

fijiSlurmPaperResults.sh: SLURM job submission script for paperResultsMaker

fijiSlurmRunHydrogel.sh: SLURM job submission script for runHydrogel

submitHydrogel: (executeable) wrapper for runHydrogel

submitPaperResults: (executeable) wrapper to paperResultsMaker

Branch info

master

Up-to-date with all paper plot routines for inital paper submission.

paper_figs

Feature branch for making the paper figures

submit_paper

Just a copy of paper_figs for the inital and final paper submission (makes it easy to quickly find important copies. Currently, it just has the initial submisssion as we are waiting for referee replies.

Directory info

• src/: src code

• runfiles/: Where runHydrogel output files go

• steadyfiles/: Where fluxODE/fluxPDE output files go

• paperData/: Where paperResultsMaker output files go

• paperInits/: Initparam files for paperResultsMaker

• paperParamInput/: Initparam files for paperResultsMaker

• paperFigs/: Where paperPlotMaker output files go