IB2d: A Matlab repository from sthavishtha

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IB2d is an Immersed Boundary Code (IB) for solving fully coupled non-linear
fluid-structure interaction models. This version of the code is based
off of Peskin's Immersed Boundary Method Paper in Acta Numerica, 2002.

Author: Nicholas A. Battista
Institution: The College of New Jersey (TCNJ)
Email: nickabattista@gmail.com
Website: http://battistn.pages.tcnj.edu
GitHub: http://www.github.com/nickabattista

HISTORY:
Date Created: May 27th, 2015 by NAB
Institution: University of North Carolina at Chapel Hill

If you use the code for research, please cite the following papers:
[1] N.A. Battista, A.J. Baird, L.A. Miller, A Mathematical Model and MATLAB Code for Muscle-Fluid-Structure Simulations, Integr. Comp. Biol. 55 (2015), 901-911.
[2] N.A. Battista, W.C. Strickland, L.A. Miller, IB2d a Python and MATLAB implementation of the immersed boundary method, Bioinspir. Biomim. 12(3):036003 (2017)
[3] N.A. Battista, W.C. Strickland, A. Barrett, L.A. Miller, IB2d Reloaded: a more powerful Python and MATLAB implementation of the immersed boundary method, Math. Meth. App. Sci., 1-26 (2017)

This code is capable of creating Lagrangian Structures using:
1. Springs (* linear, non-linear, damped *)
2. Beams (*torsional springs or non-invariant beams *)
3. Target Points
4. Muscle-Model 1 (combined Force-Length-Velocity model with a
Hill (i.e.,Length-Tension) Model )
5. 3-Element Hill Muscle (combined 3-element hill mode coupled w/
Force-Velocity/Length-Tension Model)
6. Mass Points (with or without influence of gravity)
7. Porous Structures (via Darcy’s Law)
8. Electrophysiology (FitzHugh-Nagumo coupling w/ or w/o calcium
dynamics and w/ or w/o muscle models)
9. Non-invariant Beams
10. User-defined deformation laws
11. Poroelastic Media (based on Brinkman-like forces)
12. Coagulation / Aggregation models

One is able to update those Lagrangian Structure Parameters, e.g., spring constants, resting lengths, etc

There are a number of built in Examples (~70), mostly used for teaching purposes.

If you would like us to add a specific muscle model, please contact Nick (nickabattista@gmail.edu)

If you use this code for the purposes of teaching, research, or recreation please let Nick know as well :)

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-To Run Examples:
1. Go into "Examples" Directory
2. Choose which example you want to run and enter directory
3. Type "main2d"
4. You can change input data in the input2d data folder, or modify the
geometry in the specified geometry file

-THIS VERSION HAS VARIOUS DIFFERENT FLAVORS OF EXAMPLES, e.g.,:
1. "Standard Rubberband"
ex1: - uses only linear (un-damped) springs
ex2: - uses only beams (torsional springs)
ex3: - uses only damped linear springs
ex4: - uses non-linear springs
2. "Wobbly Beam" - torsional springs between Lagrangian pts, w/ fixed ends
via target points
3. "Moving Rubberband" - rubberband moving along a zig-zag pattern, via
updating target point positions
4. "HeartTube" - examples of pumping in tubular hearts
ex1: - heart tube that pumps via muscle activation using combined
length/tension - Hill model
ex2: - heart tube that pumps via dynamic suction pumping by
changing resting lengths of springs
ex3: - heart tube that pumps via peristaltic waves of contraction
by changing resting lengths of springs
ex4: - heart tube that pumps via muscle activation by 3-element
Hill Model combined w/ length-tension/force-velocity model
ex5: - heart that pumps using an electrophysiology model, e.g. the
FitzHugh-Nagumo reduced order model of Hodgkin-Huxley
ex6: - heart that pumps using an electrophysiology model, e.g. the
FitzHugh-Nagumo reduced order model of Hodgkin-Huxley with
underlying calcium dynamics
ex7: - heart that pumps using an electrophysiology model, e.g. the
FitzHugh-Nagumo reduced order model of Hodgkin-Huxley WITH
underlying calcium dynamics WITH muscle-models
5. "Lymphangion" - tube that pumps via muscle activation using combined a
hybrid length/tension and Hill model
6. "Channel_Flow" - various channel flow examples with parabolic flow being
produced by arbitrary force on Eulerian grid
ex1: - Flow around a cylinder in a channel
ex2: - Flow around a cylinder with only one wall of channel
ex3: - Flow in a channel with a hole in the channel
ex4: - Flow produced in the middle of the channel
ex5: - Flow produced in an empty channel
ex6: - Flow in a channel, mocking an aneurysm
ex7: - Flow past cylinder with attached flag (Turek-Hron)
7. "Pulsing_Heart" - cartoon heart that "pumps" via moving target points
(interpolates between two phases)
8. "Tracers" - examples of inserting tracer particles into simulations
ex1: - Tracers in channel flow
ex2: - Tracers in an impedance pump
ex3: - Tracers in a peristaltic pump
ex4: - Tracers in bifurcating artery
9. "Mass_Points" - "adding artificial mass" to the Lagrangian structure
ex1: - 'massive' cell in pulsatile channel flow
ex2: - 'massive' cells racing due to underlying fluid velocity only!
ex3: - 'massive' cells racing under gravity only
ex4: - 'massive' cells in 'gravity vs. pulsating flow'
10. "Porous_Rubberband" - added porosity to standard rubberband problem
ex1: - Single porous rubberband example
ex2: - Comparing porous to non-porous rubberband
11. "Concentration_Gradients"
ex1: - Concentration gradient in birfuracting artery
ex2: - Pure Diffusion of Passive Scalar in Box
12. "Jellyfish_Swimming"
ex1: - Bell composed entirely of springs, motion driven by updating
resting lengths sinusoidally
ex2: - Bell composed of beams and springs
ex3: - Bell motion driven by interpolating between resting lengths
for two phases.
NOTE: not entirely debugged, yet.
13. "Vortex Induced Vibration" (VIV)
ex1: - Tethered cylinder in channel with pulsatile flow, which vibrates
due to the underlying flow.
14. "KC" - simulation using moving target points to spell out words and phrases.
ex1: - spells out a phrase to ask a girl on a date.

-It has the ability to read in Lagrangian Point Data (.vertex), Springs
(.spring), Torsional Springs (.beam), Target Pts (.target), and
Muscle Pts (.muscle), 3-Hill-Muscle-Pts (.muscle_Hill),
Tracer Particles (.tracer), Mass Points (.mass), and Porous Media
(.porous), and initial concentration (.concentration), and damped
springs (.d_spring)!

-It has the capabilitiy for updating model data:
a. updating target point positions -> Examples in Moving_Rubberband &
Pulsing_Heart
b. update_Springs() -> Examples in HeartTube
c. update_Beams() -> Examples in Jellyfish
d. update_Muscles() [can be made analogously]
e. update_Porosity() [can be made analogously]
f. update_Damped_Springs() [can be made analogously]

-It can have pseudo-inflow conditions by inducing an arbitrary force onto the
Eulerian grid (e.g., Channel Flow Examples)

-You can choose to have gravity exerting forced (yes/no) as well as prescribe
the direction of gravitational influence in any direction you'd wish,
in input2d

-You can have a background concentration gradient that is advected and diffused
via the background flow.

-You can use the Boussinesq approximation

-It can plot the following things in Matlab, if plot_Matlab flag = 1 in input2d:
a. Vorticity (colormap) + Lagrangian Pts.
b. Magnitude Velocity (colormap) + Lagrangian Pts.
c. Pressure (colormap) + Lagrangian Pts.
d. Velocity (vector form) + Lagrangian Pts.
e. Lagrangian Pts. themselves

-It has a flag for print dump interval (shared between printing to .vtk format
+ Matlab plotting)

-NOTE: This code *may* BLOW UP when Lagrangian points cross a boundary!!!!!

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-These examples print data as .vtk files, which can be read by Paraview and
VisIt.

-Every example prints the following:

viz_IB2d:

LAGRANGIAN PTS: a. Lag. Pts. themselves
b. Lag. Pts. w/ spring connections!

SCALARS (colormap): a. Vorticity
b. Magnitude of Velocity
c. uX (x-directed velocity)
d. uY (y-directed velocity)
e. Pressure
f. fMag (magnitude of force)
g. fX (magnitude of x-directed force)
h. fY (magnitude of y-directed force)

VECTORS: a. velocity data

hier_IB2d_data:

FORCE MAGNITUDES: a. fLagMag: Mag. Force on each Lag. Pt.
b. fLagNorm: Mag. Normal Force on each
Lagrangian Pt.
c. fLagTan: Tangential Force on each
Lagrangian Pt.
d. fLag_X: x-directed Forces on each Lag. Pt.
e. fLag_Y: y-directed Forces on each Lag. Pt.

TRACERS: a. tracer particle locations (*if in simulation)

-There are flags in input2d for the printing interval between saving data
-> print_Dump

-There are flags in input2d whether you'd like Matlab to plot various
quantities as simulation progresses:

-> plot_Matlab (set = 1, if yes, have Matlab plot)
-> plot_<Quantity> (set = 1, if yes for quantity)

sthavishtha/IB2d