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Questions tagged [simulation]

Simulation is the process of mimicking the behaviour of a real physical process or system using a representative model.

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3
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1answer
330 views

General case Kutta condition

I'm working on a 2D inviscid fluid simulation using a "panel method", with Potential being used to enforce the no-through boundary condition. I'm trying to incorporate the Kutta condition, which says ...
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1answer
40 views

Smoothed Particle Hydrodynamics: Weird clustering of particles. Is that normal?

I implemented a rather simple SPH simulation using a cubic-spline-kernel and a simple non-iterative pressure solver as described in this PDF in equation 9. I followed algorithm 1 of that paper (...
8
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2answers
244 views

What guidelines should I follow for simulation software projects?

I am not sure whether this question belongs here, but I would like to give it a try and benefit from the experience of the people at scicomp.SE. From my experience, the software quality in ...
3
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1answer
56 views

Computing autocorrelations of configurations in Monte Carlo simulations

In the context of Monte Carlo simulations, I am trying to learn how I should ensure that the configurations of my system are not correlated for the chosen interval of measurements. I have found out ...
3
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1answer
79 views

Calculating the Convolution Using DFT (FFT)

I have the following convolution as part of a numerical simulation. $$T(r)=\int \mathrm{d}^3r_2\, p(r_2)f(r_2)\alpha(r-r_2)\, .$$ My problem is that the analytical expressions for $f$ and $p$ do ...
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0answers
63 views

How one can simulate a system given by differential equation?

I want to simulate a diffusion environment given by the differential equation $$\frac{\partial u(x,y,t)}{\partial t}=D\left(\frac{\partial^2 u(x,y,t)}{\partial x^2}+\frac{\partial^2 u(x,y,t)}{\...
2
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1answer
61 views

Plasma Simulation Software Advice?

I’m looking for software that can simulate “hot” plasmas of multiple ion species...so some sort of simulation software that could calculate ion temperature and density distributions taking into ...
2
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1answer
124 views

Why don't we call the simulation “a model for …”?

When a set of model equations, e.g. some coupled differential equations, has solutions that behave in ways similar to real-life phenomena such as blood flow in the heart, a wave movement, or a plate ...
2
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0answers
35 views

What is the best methodology for physics simulators of large floating base rigid body systems?

I want to implement a physics simulator for large floating base rigid body systems from scratch. The Rigid Body Dynamics Systems (RBD) should typically have the following characteristics: About ~50 ...
0
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0answers
48 views

Simulate friction arround steady-state point

When simulating a friction dynamic system, I have come to a problem when approaching steady-state. In the example below, a box moves along a surface with a certain friction coefficient: ...
0
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1answer
31 views

How to implement the Impulse Based Dynamics for the rigid body dynamics simulation?

I am having hard time learning the method of impulse based dynamics developed by Mirtich for rigid body dynamics simulation. Please help me out if any body has any example code(algorithm) of it. ...
7
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4answers
194 views

Removing non-determinism from molecular dynamics code

I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing ...
2
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1answer
89 views

Multiscale Simulation of random walker

I want to simulate a system of random walkers (called A) with diffusion coefficient equal to D and other systems of random walkers (called type B) with diffusion coefficient equal to 1000 D. Second ...
2
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1answer
49 views

Symplectic linear multistep method?

I'm doing a gravitational n-body simulator and I'm thinking of implementing linear multistep methods like Adam-Bashforth. But is there any symplectic multistep methods?
4
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2answers
115 views

Is saying “math modeling and numerical simulation” wordy and redundant?

I'm describing some work on my website, and I'm wondering if my math modeling and computer simulation work is described ok: I say math modeling and numerical simulation. Should I say "...
0
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0answers
53 views

Is there a simple way of implementing dark energy into a n-body simulation?

I'm working on a gravitational n-body simulator and would like to implement dark energy into it but all I can find is papers with relativistic equations which I don't really understand. Is there a ...
3
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2answers
96 views

Optimization techniques for expensive multi-variable functions

I'm working with a finite element model in which I'm interested to minimize the average temperature at a surface. I have 15 independent variables in my model, including geometry, materials, flows, ...
1
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1answer
47 views

Harmonic oscillators with periodic boundary conditions

I am trying to simulate multiple harmonic oscillators in periodic boundary conditions (subsequently visualizing the process in VMD). I have successfully simulated multiple HOs by using the Leapfrog ...
1
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1answer
122 views

Can OpenFoam be used for interactive simulations (flying a plane)?

I'm a software engineer and I've just started to fly rc-planes. I'm currently building a self learning auto-pilot for my plane and I'm really interested in CFD. I installed OpenFOAM and ran through ...
1
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1answer
44 views

How to choose the parameters for a collision free comet trajectory

I implemented a simple simulation of a comet flying through space being deflected by the gravity of randomly generated planets for art purposes. My problem with that simulation is, that there are many ...
3
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1answer
58 views

Radiation heat transfer between surfaces

I'm trying to model the temperature distribution over a curved surface. Apart from the heat equation, I need to take into account the energy emission/absorption through electromagnetic radiation. The ...
0
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0answers
48 views

Determining the pseudo-time period of a system of $n$-pendulums via Kane's method in Python

We can use Kane's method to integrate the equations of motion for a system of $n$ pendulums with arbitrary masses and lengths (see derivation). In particular, if $(x_i,y_i)$ denotes the Cartesian ...
0
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1answer
31 views

Software for cellular automota

I would like to do simulations using cellular automata to describe the behavior of influenza. What software do you recommend?
0
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1answer
55 views

Simulating Brownian motion in 3-D for first hitting time?

I want to simulate Brownian motion in 3-D for the following conditions: $$p(x=0,y=0,z=0,t=0)=1$$ $$p(x,y,z=c,t)=0$$ where $p$ is the probability of finding molecules in the 3-D environment. I want to ...
5
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1answer
434 views

index representation of the diamond lattice

For a kinetic Monte Carlo simulation of solids that crystallize in the diamond lattice structure, I need some efficient representation of the diamond lattice as integer(s), to store it in some array-...
0
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1answer
68 views

Particle Collision to Static paticles

I have a system of particles with equal distance with each other and another at random positions which is moving with time. I want to know: a) The method by which I can reduce the number of particles ...
3
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2answers
460 views

How to simulate basic semiconductor models using the Drift-diffusion model on Python?

I'm trying to simulate basic semiconductor models for pedagogical purposes--starting from the Drift-diffusion model. Although I don't want to use an off-the-shelf semiconductor simulator--I'll be ...
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1answer
62 views

Writing parallel code for molecular computation [duplicate]

I recently moved towards computational biophysics from an experimental science background. As of now, I am learning the fundamentals and doing some basic monte carlo simulations of LJ fluid on my ...
1
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1answer
551 views

Sorting eigenvalues by the dominant contribution

[Edited to simplify the question] I am trying to associate the eigenvalues $E$ of a matrix $H$ to the original rows of the matrix. Moreover, it would be trivial to sort the eigenvalues in ascending ...
1
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1answer
70 views

Custom exponents for Lennard Jones in LAMMPS

I am trying to run an MD simulation using this generalized version of Lennard Jones. $$ U(r) = \left(\frac{r_0}{r}\right)^A -\frac{A}{B}\left( \frac{r_0}{r} \right)^B $$ However, I do not know how ...
1
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1answer
80 views

Multi-steps method for Navier-stokes equations with strongly nonlinear diffusion

I am trying to solve a particular form of the Euler / Navier-Stokes equations in 1D, with very strong and non-linear diffusion coefficients. My system of equations is \begin{cases} \...
5
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0answers
90 views

How can Navier--Stokes equations have asymmetric solutions such as Karman vortex streets

The Navier--Stokes equations are axially symmetric, so with symmetric boundary conditions, how can features such as Karman vortex streets develop? I understand that in reality symmetry does never ...
8
votes
1answer
196 views

What scientific problems can be simulated that couldn’t be simulated 10 years ago?

What scientific problems can be simulated with computers that couldn’t be simulated 10 years ago? I’m particularly interested in cutting-edge scientific simulations, which wouldn’t have been possible ...
0
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1answer
90 views

Simulation-based Optimization vs PDE-constrained Optimization

What is the difference between Simulation-based Optimization and PDE-constrained Optimization? Would studying a text on Simulation-based optimization be sufficient to understand and apply both?
1
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1answer
43 views

What are the things I should keep in mind before doing an analysis of my gromacs simulation?

I did a liquid argon simulation at 100k. I forgot during analysis that I need to accommodate for the Periodic Boundary Conditions before doing any analysis which included distance. What are other such ...
0
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1answer
56 views

Barnes-Hut method for gravitational dynamics

I have an assignment where i got this definition - "The dots velocities following the Maxwell distribution with typical velocity of $$v=<v>^{\frac{1}{2}}$$ and that mean that each of the ...
0
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2answers
132 views

Effective way to build the neighbor's list in MD

I'm trying to implement the following form of the cell/neighbor list method in my MD code. I have divided my simulation box into a fixed number of cells, and according to its positions, I have ...
2
votes
1answer
115 views

build a simple incompressible solver with spectral method

I am trying to build a simple solver for the incompressible fluid in a periodic box to learn the spectral method. I am following the textbook (Peyret R. Spectral methods for incompressible viscous ...
0
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2answers
397 views

reading and processing large GRIB files

I'm trying to convert and process GrADS (grib) files into netcdf files. The files have values every 3 hours (2890 per year), 12 z levels, 120 variables, 241 columns and 236 rows. The data is almost 80 ...
-1
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1answer
381 views

How to initiate spirals in this model?

I am trying to reproduce Tang & Othmer paper which is related to excitations and oscillations in G-protein model in Dictyostelium discoideum, an amoeba species. The mathematical model in the paper ...
1
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3answers
392 views

2D simulation of a particle with different diffusion coefficient in different directions of the particle

How can one simulate diffusion of a particle which has a natural axis and diffusion coefficient of the particle in the direction of the axis is D_1 and in perpendicular to the axis is D_2? Could ...
6
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2answers
366 views

Implementing the pressure correction method using finite elements

Ok so I am nearing the completion of my finite element Navier-Stokes solver that uses the $\theta$-method for time stepping and the pressure correction method for the pressure. I am following the ...
2
votes
1answer
271 views

MD Simulation: Reference for the Neighbor's List Method

With a rather basic knowledge in C++, I have written my own MD simulation code. Currently, I calculate forces in the most naive way: I go through all the atoms and account for their interactions. This ...
2
votes
4answers
2k views

Magnetic field simulation and visualization on Mac OS X?

Does somebody know about any tool for simulation and visualization of magnetic fields either of permanent magnets or solenoids, that can be used on Mac OS X? Maybe there is some software for Linux, ...
4
votes
2answers
211 views

Mean-squared displacement in Monte Carlo studies

Is measuring mean-squared-displacement in Monte Carlo simulations uncommon? I'm very interested to find out if this has actually ever been tried. For instance, in the context of spheres, or ...
1
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2answers
1k views

Physics Simulation in C++

OK, I know a bit of C++ (very basic syntax), and I want to do physics simulation in C++, like stuff like (also the things mentioned here): Ripples and waves over a 2-d surface Vibrating string/...
1
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0answers
46 views

Magnetostatic modelling Radia: Increasing distance between magnets a produces positive force until a certain point, beyond which force goes haywire

I have two sets of magnets. One set consists of two electromagnets (Shown below: Blue) and the other set consists of two NdFeB N40 permanent magnets. Both sets of magnets lie on the same plane. I want ...
2
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0answers
157 views

Simulation of surface tension-dominated interfaces

I want to simulate the shape of the free surface in a small fuel tank in microgravity, which is very slowly being emptied. The tank is not symmetric, the geometry is given by CAD (e.g. step file). ...
1
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1answer
95 views

Combine Hydrodynamics and Electromagnetics

Is it possible, in general, to combine hydrodynamical motion and expansion of material with, say, a finite difference time domain method to simulate light-matter interaction? If so, how is this done ...
0
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1answer
61 views

On which software can I simulate landmass collisions?

I need to be able to set the properties of the materials (density, size etc) and see what happens according to laws in Physics when landmasses collide each others, with or without bodies of water, ...