%*****************************************************************************% %***********************************% IB2d %**********************************% %*****************************************************************************% 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 :) %*****************************************************************************% %*****************************% HAPPY COMPUTING! %****************************% %*****************************************************************************% -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!!!!! %*****************************************************************************% %*******************************% VISUALIZATION %*****************************% %*****************************************************************************% -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)