# Modelling & Simulations

**URL:** https://discourse.julialang.org/c/domain/models/21.md?page=64

[Latest](https://discourse.julialang.org/latest.md) · [Categories](https://discourse.julialang.org/categories.md) · [Tags](https://discourse.julialang.org/tags.md)

**Page:** 65

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## [Simulating large nontrivial SDE systems: algorithms, reliability and speed](https://discourse.julialang.org/t/simulating-large-nontrivial-sde-systems-algorithms-reliability-and-speed/12082)

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**Author:** [@lappet](https://discourse.julialang.org/u/lappet)\
**Replies:** 7\
**Last updated:** [July 3, 2018, 7:30am UTC](https://discourse.julialang.org/t/simulating-large-nontrivial-sde-systems-algorithms-reliability-and-speed/12082 "2018-07-03T07:30:43Z")

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In short, I am interested in the simulation of large systems of nontrivial stochastic differential equations as they arise when applying phase-space methods to interacting quantum systems. As an intro example: when one …

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## [Questions on rigid body dynamics & Julia](https://discourse.julialang.org/t/questions-on-rigid-body-dynamics-julia/11968)

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**Author:** [@kyle.carbon](https://discourse.julialang.org/u/kyle.carbon)\
**Replies:** 13\
**Last updated:** [July 3, 2018, 3:29am UTC](https://discourse.julialang.org/t/questions-on-rigid-body-dynamics-julia/11968 "2018-07-03T03:29:00Z")

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Hi all! I’m just getting started with Julia. I’ll be working on motion planning algorithms and controls for rigid bodies. I’ve started to play around with various packages and had some general questions: RigidBodyDyna…

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## [Fastest way to solve Laplace equation on 3d orthogonal grids that are partially trimmed](https://discourse.julialang.org/t/fastest-way-to-solve-laplace-equation-on-3d-orthogonal-grids-that-are-partially-trimmed/11964)

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**Author:** [@aminsadeghi](https://discourse.julialang.org/u/aminsadeghi)\
**Replies:** 0\
**Last updated:** [June 26, 2018, 1:07pm UTC](https://discourse.julialang.org/t/fastest-way-to-solve-laplace-equation-on-3d-orthogonal-grids-that-are-partially-trimmed/11964 "2018-06-26T13:07:16Z")

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I’m trying to solve the Laplace equation in 3d on orthogonal grids that are partially trimmed, i.e. some of the internal grid points are removed from the domain. These grids come from micro-ct tomography images and corre…

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## [Way to automatically distinguish branch of roots in parametric sweep?](https://discourse.julialang.org/t/way-to-automatically-distinguish-branch-of-roots-in-parametric-sweep/11732)

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**Author:** [@djsegal](https://discourse.julialang.org/u/djsegal)\
**Replies:** 7\
**Last updated:** [June 22, 2018, 10:26pm UTC](https://discourse.julialang.org/t/way-to-automatically-distinguish-branch-of-roots-in-parametric-sweep/11732 "2018-06-22T22:26:59Z")

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Let’s say you have some nonlinear function that you plug into a root solver to get all the roots // where the maximum number of real roots possible \<= N (i.e. N = 3) Then you sweep this function over M other values to …

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## [Discrepancy between .~ and .==false for BitArrays](https://discourse.julialang.org/t/discrepancy-between-and-false-for-bitarrays/11787)

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**Author:** [@tyleransom](https://discourse.julialang.org/u/tyleransom)\
**Replies:** 2\
**Last updated:** [June 19, 2018, 4:57pm UTC](https://discourse.julialang.org/t/discrepancy-between-and-false-for-bitarrays/11787 "2018-06-19T16:57:37Z")

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Hi, I’m having trouble understanding why the following don’t yield equivalent objects: srand(1234) x = rand(50,1); y=rand(50,1).\>0.5; z=rand(50,1).\>0.5; size(x\[.~y .& .~z\]) size(x\[y.==false .& z.==false\]) size(x\[.~y\])…

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## [Avoiding Plotting to dense plots, saveat not working](https://discourse.julialang.org/t/avoiding-plotting-to-dense-plots-saveat-not-working/9540)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 8\
**Last updated:** [May 24, 2018, 9:18am UTC](https://discourse.julialang.org/t/avoiding-plotting-to-dense-plots-saveat-not-working/9540 "2018-05-24T09:18:17Z")

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I am running simulations of SDEs and plotting the results. I keep having problem that Jupyter crashes, despite that the simulations shouldn’t be that intense. I think hat I have tracked the problems to the plots being to…

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## [Matrix-free linear solvers for DifferentialEquations.jl](https://discourse.julialang.org/t/matrix-free-linear-solvers-for-differentialequations-jl/10968)

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**Author:** [@tobydriscoll](https://discourse.julialang.org/u/tobydriscoll)\
**Replies:** 4\
**Last updated:** [May 18, 2018, 6:31pm UTC](https://discourse.julialang.org/t/matrix-free-linear-solvers-for-differentialequations-jl/10968 "2018-05-18T18:31:58Z")

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I’m trying to solve a DAE (mass matrix form) for a 2D spectral discretization. The number of DOF is going to be large, and the Jacobian, which I compute explicitly, is not especially sparse. I’d like to use a preconditi…

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## [How to read a system of equations?](https://discourse.julialang.org/t/how-to-read-a-system-of-equations/10207)

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**Author:** [@tomj](https://discourse.julialang.org/u/tomj)\
**Replies:** 5\
**Last updated:** [April 7, 2018, 1:13pm UTC](https://discourse.julialang.org/t/how-to-read-a-system-of-equations/10207 "2018-04-07T13:13:13Z")

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Hello Julia users! I’m a beginner in Julia, and am currently blocked with the following problem. Imagine a system of equations like x(t) = c1 + c2\*x(t-1) + c3\*y(t-1) y(t) = c4 + c5\*y(t-1) + c6\*x(t-1) I would like t…

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## [JuAFEM + ForwardDiff + NLsolve = Finite elements for nonlinear problems?](https://discourse.julialang.org/t/juafem-forwarddiff-nlsolve-finite-elements-for-nonlinear-problems/10085)

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**Author:** [@louisponet](https://discourse.julialang.org/u/louisponet)\
**Replies:** 53\
**Last updated:** [April 4, 2018, 9:56pm UTC](https://discourse.julialang.org/t/juafem-forwarddiff-nlsolve-finite-elements-for-nonlinear-problems/10085 "2018-04-04T21:56:42Z")

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Hi, I’m in the process of solving a Landau theory model concerning a crystal where strain and electric polarization are coupled. I’m trying to minimize the total free energy given by: F = Fl(P, α) + Fc(ε, C) + Fq(P, ε,…

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## [Get error when solving SDEs after last update](https://discourse.julialang.org/t/get-error-when-solving-sdes-after-last-update/10137)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 3\
**Last updated:** [April 4, 2018, 1:25pm UTC](https://discourse.julialang.org/t/get-error-when-solving-sdes-after-last-update/10137 "2018-04-04T13:25:54Z")

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I tried rerunning my code after the latest 4.2 update to the DifferentialEquations package. I use the reaction\_network DSL from DiffEqBiological package, from these I generate and solve SDEs with non-diagonal noise. Howe…

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## [Avoiding high plotting densities when plotting Solutions to SDE with small time steps](https://discourse.julialang.org/t/avoiding-high-plotting-densities-when-plotting-solutions-to-sde-with-small-time-steps/9168)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 8\
**Last updated:** [April 1, 2018, 9:04am UTC](https://discourse.julialang.org/t/avoiding-high-plotting-densities-when-plotting-solutions-to-sde-with-small-time-steps/9168 "2018-04-01T09:04:37Z")

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I am looking at a biochemical reaction networks and how it behaves under noise. The code looks something like: gr() ... prob\_sde = SDEProblem(model,u0,(0.,1000.)) sol = solve(prob\_sde,ImplicitEM(),dt=1//2^(7),callback=c…

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## [Parallel Monte Carlo Simulations](https://discourse.julialang.org/t/parallel-monte-carlo-simulations/9692)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 0\
**Last updated:** [March 13, 2018, 5:58pm UTC](https://discourse.julialang.org/t/parallel-monte-carlo-simulations/9692 "2018-03-13T17:58:06Z")

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I am simulating a large number of SDEs and looking at the results. Things starts to take quite a while and I figured that I had 8 cores on my computer, might as well try to use them. Unfortunate I cannot get things to wo…

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## [Interest for DFT simulations job control package?](https://discourse.julialang.org/t/interest-for-dft-simulations-job-control-package/9546)

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**Author:** [@louisponet](https://discourse.julialang.org/u/louisponet)\
**Replies:** 10\
**Last updated:** [March 10, 2018, 8:34am UTC](https://discourse.julialang.org/t/interest-for-dft-simulations-job-control-package/9546 "2018-03-10T08:34:19Z")

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Hi all, I’ve worked on a package that automates a lot of tedious work one has to do when working with Density Functional Theory packages/simulations. It’s pretty fully featured, although ofcourse a lot extra could be ad…

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## [Saving Differential Equations Solutions to disk](https://discourse.julialang.org/t/saving-differential-equations-solutions-to-disk/9387)

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**Author:** [@FHell](https://discourse.julialang.org/u/FHell)\
**Replies:** 3\
**Last updated:** [February 28, 2018, 2:05pm UTC](https://discourse.julialang.org/t/saving-differential-equations-solutions-to-disk/9387 "2018-02-28T14:05:55Z")

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Hi everyone, I want to generate an ensemble of Solutions to a differential equation to later study more in depth, so I want to save it to disk (keeping it simple: one file per simulation. Each solution is about 100Mb). …

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## [Controlsystem.jl : how to mix continuous and discrete time transfer functions](https://discourse.julialang.org/t/controlsystem-jl-how-to-mix-continuous-and-discrete-time-transfer-functions/8894)

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**Author:** [@bo-lo](https://discourse.julialang.org/u/bo-lo)\
**Replies:** 4\
**Last updated:** [February 20, 2018, 11:28pm UTC](https://discourse.julialang.org/t/controlsystem-jl-how-to-mix-continuous-and-discrete-time-transfer-functions/8894 "2018-02-20T23:28:33Z")

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I am using Julia 0.5.2 I am modeling a continuous time RLC circuit in the s domain. I am modeling a digital controller in the z domain. I tried multiplying the 2 transfer functions together to get the open loop transfe…

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## [Making a callback event at a single timepoint](https://discourse.julialang.org/t/making-a-callback-event-at-a-single-timepoint/9038)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 4\
**Last updated:** [February 13, 2018, 4:44pm UTC](https://discourse.julialang.org/t/making-a-callback-event-at-a-single-timepoint/9038 "2018-02-13T16:44:51Z")

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Simple question. At a certain timepoint (e.g. t = 100) I want to make a callback, changing a parameter or variable value. The most intuitive way would be function condition(u,t,integrator) t == 100 end however the…

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## [Events that changes parameter values](https://discourse.julialang.org/t/events-that-changes-parameter-values/9015)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 4\
**Last updated:** [February 13, 2018, 4:01pm UTC](https://discourse.julialang.org/t/events-that-changes-parameter-values/9015 "2018-02-13T16:01:24Z")

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I am running simulations on chemical reaction systems. Usually for these I have some input signal and I want to investigate what happens to the system when suddenly an input is turned on. Typically I might have a variabl…

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## [How to handle simple events like step functions?](https://discourse.julialang.org/t/how-to-handle-simple-events-like-step-functions/8926)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 4\
**Last updated:** [February 8, 2018, 5:08pm UTC](https://discourse.julialang.org/t/how-to-handle-simple-events-like-step-functions/8926 "2018-02-08T17:08:41Z")

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Hello, In one paragraph I am trying to solve differential equations with discontinuities by solving them up to the discontinuity, change my system and input the old solution as initial conditions to a new problem. This…

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## [Running an ODEProblem until given a signal](https://discourse.julialang.org/t/running-an-odeproblem-until-given-a-signal/8913)

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**Author:** [@mindbound](https://discourse.julialang.org/u/mindbound)\
**Replies:** 2\
**Last updated:** [February 7, 2018, 11:51pm UTC](https://discourse.julialang.org/t/running-an-odeproblem-until-given-a-signal/8913 "2018-02-07T23:51:02Z")

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Is it possible for the timespan of an ODEProblem to be open-ended, i.e. for the problem to run until given an external signal (possibly via a discrete callback with an appropriate condition)? Intuitively, this would mean…

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## [Using results from ODEProblem while it is running](https://discourse.julialang.org/t/using-results-from-odeproblem-while-it-is-running/8874)

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**Author:** [@mindbound](https://discourse.julialang.org/u/mindbound)\
**Replies:** 2\
**Last updated:** [February 7, 2018, 1:55am UTC](https://discourse.julialang.org/t/using-results-from-odeproblem-while-it-is-running/8874 "2018-02-07T01:55:39Z")

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Hello all, I’m currently studying the documentation of DifferentialEquations.jl and trying to port my older computational neuroscience codes for using it instead of my own, less elegant and performant, ODE solvers. Whil…

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## [Trouble with ControlSystems.jl](https://discourse.julialang.org/t/trouble-with-controlsystems-jl/8783)

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**Author:** [@bo-lo](https://discourse.julialang.org/u/bo-lo)\
**Replies:** 13\
**Last updated:** [February 6, 2018, 1:21am UTC](https://discourse.julialang.org/t/trouble-with-controlsystems-jl/8783 "2018-02-06T01:21:01Z")

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Hi I am trying to use ControlSystems.jl to model circuits involving inductors, capacitors and resistances in the s domain. On my first try, I am getting a Zero denominator issue that I cannot debug. Here is the code (J…

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## [Stochastic solver pushes chemical langevin equations into negative concentrations](https://discourse.julialang.org/t/stochastic-solver-pushes-chemical-langevin-equations-into-negative-concentrations/8688)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 3\
**Last updated:** [January 31, 2018, 2:08pm UTC](https://discourse.julialang.org/t/stochastic-solver-pushes-chemical-langevin-equations-into-negative-concentrations/8688 "2018-01-31T14:08:14Z")

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Summary: When I simulate the stochastic time development of a reaction network the simulation crashes due to concentrations becoming negative (works fine for deterministic solution). I have this chemical reaction networ…

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## [Solving Stochastic Differential Equations with Same Random Numbers](https://discourse.julialang.org/t/solving-stochastic-differential-equations-with-same-random-numbers/8189)

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**Author:** [@Torkel](https://discourse.julialang.org/u/Torkel)\
**Replies:** 3\
**Last updated:** [January 7, 2018, 11:06am UTC](https://discourse.julialang.org/t/solving-stochastic-differential-equations-with-same-random-numbers/8189 "2018-01-07T11:06:56Z")

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One Line Question: How do I use Julia to solve a system of Stochastic Differential Equations were there are correlated terms of noise (or “the same” noise appears in several places) Biological Background: Lets say I hav…

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## [Introducing a new Control Toolbox for Julia with Interactive root locus](https://discourse.julialang.org/t/introducing-a-new-control-toolbox-for-julia-with-interactive-root-locus/7486)

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**Author:** [@Ronis\_BR](https://discourse.julialang.org/u/Ronis_BR)\
**Replies:** 13\
**Last updated:** [December 5, 2017, 12:45pm UTC](https://discourse.julialang.org/t/introducing-a-new-control-toolbox-for-julia-with-interactive-root-locus/7486 "2017-12-05T12:45:12Z")

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Hi guys! I finally decided to publish a Control Toolbox we were developing at my institution. I know that there are a few alternatives already coded in Julia, but we wanted something more specific. We wanted that the co…

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## [Dynamical Systems API and ChaosTools.jl](https://discourse.julialang.org/t/dynamical-systems-api-and-chaostools-jl/4041)

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**Author:** [@Datseris](https://discourse.julialang.org/u/Datseris)\
**Replies:** 22\
**Last updated:** [October 1, 2017, 11:29am UTC](https://discourse.julialang.org/t/dynamical-systems-api-and-chaostools-jl/4041 "2017-10-01T11:29:35Z")

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I have recently started on a journey to create a package ChaosTools.jl that has common useful tools used in the study of nonlinear dynamics and chaos, like e.g. lyapunov exponents, attractor dimension estimation and othe…

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## [Announcing DynamicalSystems.jl & Inviting for JuliaDynamics](https://discourse.julialang.org/t/announcing-dynamicalsystems-jl-inviting-for-juliadynamics/5613)

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**Author:** [@Datseris](https://discourse.julialang.org/u/Datseris)\
**Replies:** 11\
**Last updated:** [August 28, 2017, 9:48pm UTC](https://discourse.julialang.org/t/announcing-dynamicalsystems-jl-inviting-for-juliadynamics/5613 "2017-08-28T21:48:31Z")

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Hi all. I have been working on a package on my free time that I have mentioned in a previous post in this category. Now it is at a decent state and has been accepted as a Julia package. It’s called DynamicalSystems.jl! W…

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## [ODE Solver with ApproxFun's that change over time](https://discourse.julialang.org/t/ode-solver-with-approxfuns-that-change-over-time/3379)

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**Author:** [@anodos](https://discourse.julialang.org/u/anodos)\
**Replies:** 2\
**Last updated:** [April 26, 2017, 3:23pm UTC](https://discourse.julialang.org/t/ode-solver-with-approxfuns-that-change-over-time/3379 "2017-04-26T15:23:17Z")

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Hi, I’m looking for an ODE solver that can solve DE’s of the form: dydt = f(t,y) where the ‘y’ are themselves ApproxFun functions (i.e. Chebychev interpolations of a function.) A very simple example might be the funct…

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## [Modeling concurrency](https://discourse.julialang.org/t/modeling-concurrency/3172)

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**Author:** [@bo-lo](https://discourse.julialang.org/u/bo-lo)\
**Replies:** 2\
**Last updated:** [April 12, 2017, 1:07pm UTC](https://discourse.julialang.org/t/modeling-concurrency/3172 "2017-04-12T13:07:54Z")

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Hi I am just starting with Julia and would like to model concurrency as in digital circuits. A trivial example would be to model a 3 bit counter and see its output in a waveform viewer. A more evolved example would be …

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## [DynamicalBilliards.jl : A Julia package for Dynamical Billiard systems in two dimensions](https://discourse.julialang.org/t/dynamicalbilliards-jl-a-julia-package-for-dynamical-billiard-systems-in-two-dimensions/1826)

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**Author:** [@Datseris](https://discourse.julialang.org/u/Datseris)\
**Replies:** 0\
**Last updated:** [February 1, 2017, 7:32pm UTC](https://discourse.julialang.org/t/dynamicalbilliards-jl-a-julia-package-for-dynamical-billiard-systems-in-two-dimensions/1826 "2017-02-01T19:32:21Z")

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DynamicalBilliards.jl is a Julia package written entirely in Julia, which simulates dynamical billiards systems. The current release version is fully usable and close to being complete! The package is easy-to-use, modul…

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