# Modelling & Simulations

**URL:** https://discourse.julialang.org/c/domain/models/21.md?page=50

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**Page:** 51

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## [Write-out simulation data from Julia to other file formats (JSON, …)](https://discourse.julialang.org/t/write-out-simulation-data-from-julia-to-other-file-formats-json/73341)

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**Author:** [@Chimel](https://discourse.julialang.org/u/Chimel)\
**Replies:** 2\
**Last updated:** [December 19, 2021, 7:27pm UTC](https://discourse.julialang.org/t/write-out-simulation-data-from-julia-to-other-file-formats-json/73341 "2021-12-19T19:27:10Z")

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Hello, Is there a tool/method to write-out simulation data to other formats such as: JSON, yaml, xml, text files, csv, vdb, alembic (abc), lossless image file, exr, fbx, obj, gltf, hdf5? So that it can be imported into…

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## [How to reality-chek a working ODE model made with DifferentialEquations?](https://discourse.julialang.org/t/how-to-reality-chek-a-working-ode-model-made-with-differentialequations/73190)

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**Author:** [@Luigi\_Marongiu](https://discourse.julialang.org/u/Luigi_Marongiu)\
**Replies:** 1\
**Last updated:** [December 16, 2021, 11:26am UTC](https://discourse.julialang.org/t/how-to-reality-chek-a-working-ode-model-made-with-differentialequations/73190 "2021-12-16T11:26:43Z")

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Hello, I have made a simulation of bacterial infection. I am focusing on the induction of phages. The system works but I am not sure about the results. Even if I activate 400 000 hosts at t=250 (that is, 96.6% of the ba…

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## [Looking for modeling ideas](https://discourse.julialang.org/t/looking-for-modeling-ideas/73013)

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**Author:** [@Emmanuel-R8](https://discourse.julialang.org/u/Emmanuel-R8)\
**Replies:** 3\
**Last updated:** [December 13, 2021, 6:44pm UTC](https://discourse.julialang.org/t/looking-for-modeling-ideas/73013 "2021-12-13T18:44:42Z")

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Hi - I have experience in MTK, Flux and Turing. I have used them in pairs. BUT, I have never used them all three at the same time. I have been looking for easy-ish ideas (think blogpost level) that I could use to educa…

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## [Problem defining Continuos Dynamical Systems](https://discourse.julialang.org/t/problem-defining-continuos-dynamical-systems/73009)

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**Author:** [@pafloxy](https://discourse.julialang.org/u/pafloxy)\
**Replies:** 2\
**Last updated:** [December 13, 2021, 10:47am UTC](https://discourse.julialang.org/t/problem-defining-continuos-dynamical-systems/73009 "2021-12-13T10:47:16Z")

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I am having a problem defining the Rossler system using the following way~ ##eom~~ @inline @inbounds function rossler\_eom( u, p, t) a = p\[1\]; b = p\[2\]; c = p\[3\] du1 = -u\[2\] - u\[3\] du2 = u…

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## [Analogue to lyapunov exponents](https://discourse.julialang.org/t/analogue-to-lyapunov-exponents/70264)

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**Author:** [@pafloxy](https://discourse.julialang.org/u/pafloxy)\
**Replies:** 2\
**Last updated:** [December 13, 2021, 7:21am UTC](https://discourse.julialang.org/t/analogue-to-lyapunov-exponents/70264 "2021-12-13T07:21:22Z")

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Hi! While using the usual lyapunov function from the DynamicalSystems.jl package measures the rate of exponential separation of two slightly perturbed trajectories, I would instead like to measure the rate of exponentia…

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## [ExtraVariableSystemException while working with DiffEqOperators.jl](https://discourse.julialang.org/t/extravariablesystemexception-while-working-with-diffeqoperators-jl/72535)

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**Author:** [@youainti](https://discourse.julialang.org/u/youainti)\
**Replies:** 2\
**Last updated:** [December 6, 2021, 11:39pm UTC](https://discourse.julialang.org/t/extravariablesystemexception-while-working-with-diffeqoperators-jl/72535 "2021-12-06T23:39:03Z")

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I’ve run into two issues while using DiffEqOperators.jl to solve the Feynman-Kac Formula through the method of lines. Here is the setup to the problem: #setup symbols @parameters τ y @variables f(..) Dτ = Differential(…

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## [What are some recommended ways to create networks of ensembles of neurons?](https://discourse.julialang.org/t/what-are-some-recommended-ways-to-create-networks-of-ensembles-of-neurons/72673)

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**Author:** [@yohan](https://discourse.julialang.org/u/yohan)\
**Replies:** 0\
**Last updated:** [December 6, 2021, 6:35pm UTC](https://discourse.julialang.org/t/what-are-some-recommended-ways-to-create-networks-of-ensembles-of-neurons/72673 "2021-12-06T18:35:18Z")

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Hi! I’m very new to Julia and considering migrating my Izhikevich neuronal network simulations to Julia from MATLAB. I was wondering about ways of implementing interactions among ensembles of units. I’d like to have pop…

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## [Trouble with DifferentialEquations.jl using MPI with the integrator interface](https://discourse.julialang.org/t/trouble-with-differentialequations-jl-using-mpi-with-the-integrator-interface/70356)

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**Author:** [@reidr](https://discourse.julialang.org/u/reidr)\
**Replies:** 10\
**Last updated:** [December 2, 2021, 7:46am UTC](https://discourse.julialang.org/t/trouble-with-differentialequations-jl-using-mpi-with-the-integrator-interface/70356 "2021-12-02T07:46:56Z")

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I’m using DIfferentialEquations.jl to solve a very large (10^9) system of coupled ODEs. I’m using MPI because the memory required for the full system won’t find on a workstation. The problem fits pretty naturally with th…

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## [Help with ModelingToolkit](https://discourse.julialang.org/t/help-with-modelingtoolkit/72328)

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**Author:** [@contradict](https://discourse.julialang.org/u/contradict)\
**Replies:** 2\
**Last updated:** [December 1, 2021, 6:14pm UTC](https://discourse.julialang.org/t/help-with-modelingtoolkit/72328 "2021-12-01T18:14:39Z")

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I am playing with the continuous\_events feature in ModelingToolkit and have gotten stuck. My current example is here. With ModelingToolkit 7.1.3, running limit\_example() produces the error ERROR: AssertionError: maximum…

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## [Concept of continuous depths for neural networks in UDEs](https://discourse.julialang.org/t/concept-of-continuous-depths-for-neural-networks-in-udes/72090)

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**Author:** [@saadfaizan](https://discourse.julialang.org/u/saadfaizan)\
**Replies:** 7\
**Last updated:** [November 30, 2021, 5:52am UTC](https://discourse.julialang.org/t/concept-of-continuous-depths-for-neural-networks-in-udes/72090 "2021-11-30T05:52:33Z")

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I recently came across the concept of continuous depth in Neural ODEs. I was wondering if the neural networks in the UDE framework have a similar concept of continuous depths. @ChrisRackauckas

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## [Flexible workflow for altering the equations of a dynamical system / diffeq](https://discourse.julialang.org/t/flexible-workflow-for-altering-the-equations-of-a-dynamical-system-diffeq/71390)

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**Author:** [@Datseris](https://discourse.julialang.org/u/Datseris)\
**Replies:** 12\
**Last updated:** [November 24, 2021, 2:54pm UTC](https://discourse.julialang.org/t/flexible-workflow-for-altering-the-equations-of-a-dynamical-system-diffeq/71390 "2021-11-24T14:54:41Z")

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Hi all, kind of organizational equation. I have a dynamical system whose equations I change frequently. I add and remove different dynamical components and connections. I’m in a pretty exploratory stage. It becomes real…

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## [Packages for kinematic trees?](https://discourse.julialang.org/t/packages-for-kinematic-trees/55963)

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**Author:** [@airpmb](https://discourse.julialang.org/u/airpmb)\
**Replies:** 3\
**Last updated:** [November 24, 2021, 3:34am UTC](https://discourse.julialang.org/t/packages-for-kinematic-trees/55963 "2021-11-24T03:34:58Z")

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tl;dr: Any good packages for defining trees of named homogeneous transforms? I have a use case and wonder if someone here might help accelerate my search for existing solutions that I can adopt or build upon. Basically …

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## [Implementing the Social Force Model from Helbing 1995](https://discourse.julialang.org/t/implementing-the-social-force-model-from-helbing-1995/71960)

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**Author:** [@jacobusmmsmit](https://discourse.julialang.org/u/jacobusmmsmit)\
**Replies:** 12\
**Last updated:** [November 23, 2021, 10:54pm UTC](https://discourse.julialang.org/t/implementing-the-social-force-model-from-helbing-1995/71960 "2021-11-23T22:54:45Z")

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Hey everyone, I’m trying to implement the social force model for pedestrian dynamics, which models pedestrians using physics. I’m not sure what the best course of action is, specifically in terms of which packages I coul…

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## [PDEsystems has version conflict?](https://discourse.julialang.org/t/pdesystems-has-version-conflict/71871)

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**Author:** [@Goosee](https://discourse.julialang.org/u/Goosee)\
**Replies:** 17\
**Last updated:** [November 22, 2021, 11:04pm UTC](https://discourse.julialang.org/t/pdesystems-has-version-conflict/71871 "2021-11-22T23:04:43Z")

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I am new to Julia. I installed today the latest version of Julia, Atom and Juno and the packages to run the examples on the NeuralPDE.jl website. I cannot run any command from the package ModelingToolkit that uses “PDESy…

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## [Position Based Dynamics](https://discourse.julialang.org/t/position-based-dynamics/70559)

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**Author:** [@vpuri3](https://discourse.julialang.org/u/vpuri3)\
**Replies:** 3\
**Last updated:** [November 18, 2021, 6:42am UTC](https://discourse.julialang.org/t/position-based-dynamics/70559 "2021-11-18T06:42:42Z")

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hi all, I’m new to robotics and was wondering if anybody has thoughts on Position Based Dynamics methods: https://matthias-research.github.io/pages/publications/smallsteps.pdf. They seem to be able to account for constra…

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## [Problem understanding results of DiffEqUncertainty](https://discourse.julialang.org/t/problem-understanding-results-of-diffequncertainty/71193)

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**Author:** [@MrBellamy](https://discourse.julialang.org/u/MrBellamy)\
**Replies:** 7\
**Last updated:** [November 15, 2021, 1:57pm UTC](https://discourse.julialang.org/t/problem-understanding-results-of-diffequncertainty/71193 "2021-11-15T13:57:55Z")

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I have issues using the librairie DiffEqUncertainty.jl or at least understanding the results. I have a DAE made of 4 differential equations and 1 algebric equations. I defined it using a mass matrix and I am solving it …

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## [How to simulate the average trajectories of the SDE variables?](https://discourse.julialang.org/t/how-to-simulate-the-average-trajectories-of-the-sde-variables/71378)

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**Author:** [@rimi](https://discourse.julialang.org/u/rimi)\
**Replies:** 2\
**Last updated:** [November 12, 2021, 3:47pm UTC](https://discourse.julialang.org/t/how-to-simulate-the-average-trajectories-of-the-sde-variables/71378 "2021-11-12T15:47:34Z")

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Hello, I have a code to solve to SDEs I am working on, in R. The equations in question are, dX = (-X\*a + (Y-X)b + h)dt + g dW and dY = (-Ya + (X-Y)\*b)dt for time \[0,200\], a=0.30, b=0.2, g=1 and h is 1 for time \[50,70\] …

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## [Plotting in phase space with Makie.jl](https://discourse.julialang.org/t/plotting-in-phase-space-with-makie-jl/70652)

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**Author:** [@baumer](https://discourse.julialang.org/u/baumer)\
**Replies:** 3\
**Last updated:** [November 11, 2021, 2:05pm UTC](https://discourse.julialang.org/t/plotting-in-phase-space-with-makie-jl/70652 "2021-11-11T14:05:46Z")

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I have an 10-element Vector{Array{Float64, 6}}: that gives the solution to a 6D + time PDE at every point in phase space on a certain interval as it progress through 10 time steps (hence the 10-element vector). I want t…

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## [How to custom noise](https://discourse.julialang.org/t/how-to-custom-noise/71280)

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**Author:** [@Frazze](https://discourse.julialang.org/u/Frazze)\
**Replies:** 6\
**Last updated:** [November 11, 2021, 12:20pm UTC](https://discourse.julialang.org/t/how-to-custom-noise/71280 "2021-11-11T12:20:32Z")

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Hi everyone, I would like to study a SDE Problem with just additive white gaussian noise, but I would like also to control the value of the variance just to see what happen varying this value. How can I do? How can bui…

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## [CTESN Code / Packages?](https://discourse.julialang.org/t/ctesn-code-packages/71279)

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**Author:** [@wkharold](https://discourse.julialang.org/u/wkharold)\
**Replies:** 0\
**Last updated:** [November 10, 2021, 6:48pm UTC](https://discourse.julialang.org/t/ctesn-code-packages/71279 "2021-11-10T18:48:32Z")

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I’m looking for the code used in the Continuous-Time Echo State Network paper. Surrogages.jl is referenced in the paper, and I found the ReservoirComputing.jl package but on first glance neither illustrates how to get th…

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## [\[Article\] Using Julia to compare evolutionary game theory to agent based modelling](https://discourse.julialang.org/t/article-using-julia-to-compare-evolutionary-game-theory-to-agent-based-modelling/59809)

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**Author:** [@jacobusmmsmit](https://discourse.julialang.org/u/jacobusmmsmit)\
**Replies:** 5\
**Last updated:** [November 10, 2021, 2:14pm UTC](https://discourse.julialang.org/t/article-using-julia-to-compare-evolutionary-game-theory-to-agent-based-modelling/59809 "2021-11-10T14:14:41Z")

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Hello all, I recently completed an undergraduate research project with Warwick’s Data Science Society. I had an idea to compare simulation to analytic methods while writing an essay for one of my economics modules and I …

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## [Tutorial on Coupling Jumps](https://discourse.julialang.org/t/tutorial-on-coupling-jumps/70957)

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**Author:** [@tom-plaa](https://discourse.julialang.org/u/tom-plaa)\
**Replies:** 0\
**Last updated:** [November 4, 2021, 2:42pm UTC](https://discourse.julialang.org/t/tutorial-on-coupling-jumps/70957 "2021-11-04T14:42:36Z")

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Didn’t create an issue on the repo because this might be just my interpretation being wrong. I am trying to run code based on the tutorial at Jump Diffusion page. It mentions that this is supposed to be a Cox process (…

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## [Differentiate through solve for a subset of parameters](https://discourse.julialang.org/t/differentiate-through-solve-for-a-subset-of-parameters/70869)

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**Author:** [@hexaeder](https://discourse.julialang.org/u/hexaeder)\
**Replies:** 5\
**Last updated:** [November 4, 2021, 11:07am UTC](https://discourse.julialang.org/t/differentiate-through-solve-for-a-subset-of-parameters/70869 "2021-11-04T11:07:33Z")

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If I pass a vector of dual numbers as parameters, the solver will recocnize the dual numbers and provide a vector dx\<:Vector{Dual...} to my diff eq function. In my problem I have several parameters I want to tune but a…

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## [Restricting "active" joints in RigidBodyDynamics.jl](https://discourse.julialang.org/t/restricting-active-joints-in-rigidbodydynamics-jl/70829)

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**Author:** [@benjamin-macadam](https://discourse.julialang.org/u/benjamin-macadam)\
**Replies:** 0\
**Last updated:** [November 2, 2021, 10:19pm UTC](https://discourse.julialang.org/t/restricting-active-joints-in-rigidbodydynamics-jl/70829 "2021-11-02T22:19:15Z")

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Hi there, I have been using RigidBodyDynamics.jl to do some simulations with robotics for about a month or so. I’m finding performance for some of my simulations really suffers when I use the full collection of joints i…

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## [Computing the Lyapunov exponent of the Hénon map with DynamicalSystems.jl](https://discourse.julialang.org/t/computing-the-lyapunov-exponent-of-the-henon-map-with-dynamicalsystems-jl/70810)

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**Author:** [@NoFishLikeIan](https://discourse.julialang.org/u/NoFishLikeIan)\
**Replies:** 2\
**Last updated:** [November 2, 2021, 3:25pm UTC](https://discourse.julialang.org/t/computing-the-lyapunov-exponent-of-the-henon-map-with-dynamicalsystems-jl/70810 "2021-11-02T15:25:56Z")

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Issue I am trying to compute the Lyapunov exponent of the Hénon map with b = 0.3 and a = 1.8 but the lyapunov function from DynamicalSystems.jl seems to not converge. Is there something I am doing wrong or is this expect…

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## [Solving semilinear ODE with changing linear operator](https://discourse.julialang.org/t/solving-semilinear-ode-with-changing-linear-operator/70747)

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**Author:** [@wsshin](https://discourse.julialang.org/u/wsshin)\
**Replies:** 3\
**Last updated:** [November 1, 2021, 8:47pm UTC](https://discourse.julialang.org/t/solving-semilinear-ode-with-changing-linear-operator/70747 "2021-11-01T20:47:19Z")

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I am trying to solve a semilinear ODE whose linear operator depends on the solution: du/dt = A(u) u + f(u,t). The “linear” operator A(u) is diagonal. I am wondering what is the best approach to solve this problem by Di…

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## [Implementing Dry friction in modeling toolkit](https://discourse.julialang.org/t/implementing-dry-friction-in-modeling-toolkit/70743)

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**Author:** [@yjr](https://discourse.julialang.org/u/yjr)\
**Replies:** 1\
**Last updated:** [November 1, 2021, 4:38pm UTC](https://discourse.julialang.org/t/implementing-dry-friction-in-modeling-toolkit/70743 "2021-11-01T16:38:30Z")

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Hello, I would like to implement some function to have components simulating dry friction with modeling toolkit. As a starting point, I think the implementation from modelica is quite good. Most of it can be implemented…

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## [DAEs and Turing](https://discourse.julialang.org/t/daes-and-turing/70651)

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**Author:** [@BLI](https://discourse.julialang.org/u/BLI)\
**Replies:** 9\
**Last updated:** [October 31, 2021, 4:11pm UTC](https://discourse.julialang.org/t/daes-and-turing/70651 "2021-10-31T16:11:28Z")

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1. Model and DifferentialEquations I’m trying to estimate initial values and parameters in a DAE using Turing. The structure of the DAE is as follows: \\frac{dx}{dt} = f(x,z,u;\\theta) \\\\ 0 = g(x,z,u;\\theta) I have avai…

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## [Weird Schrodinger solution by DifferentialEquations.jl versus time interval](https://discourse.julialang.org/t/weird-schrodinger-solution-by-differentialequations-jl-versus-time-interval/70542)

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**Author:** [@TravellingLight6](https://discourse.julialang.org/u/TravellingLight6)\
**Replies:** 2\
**Last updated:** [October 28, 2021, 12:53pm UTC](https://discourse.julialang.org/t/weird-schrodinger-solution-by-differentialequations-jl-versus-time-interval/70542 "2021-10-28T12:53:16Z")

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Suppose we want to solve a simple schrodinger equation under columb potential,namely, \\Psi''=(V-E)\\Psi and V(r)=-\\frac{1}{r}, The wavefunction u(r) of ground state is: \\sim a\\times r\\cdot e^{-br} which should be the ex…

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## [Confusion on DifferentialEquations.jl. How many saved timesteps](https://discourse.julialang.org/t/confusion-on-differentialequations-jl-how-many-saved-timesteps/70409)

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**Author:** [@DerOzean](https://discourse.julialang.org/u/DerOzean)\
**Replies:** 5\
**Last updated:** [October 27, 2021, 11:00am UTC](https://discourse.julialang.org/t/confusion-on-differentialequations-jl-how-many-saved-timesteps/70409 "2021-10-27T11:00:42Z")

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Hello everyone, I’m working on a dynamic food web and solving some differential equations. As solver I’m using the DP5 monte carlo method. After successful solving the problem I get for every time steps 4 time the same…

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