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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141 views

What is the time_step and how many iterations required for convergence purpose in fluids simulation [closed]

My question seems elementary: I use a new numerical method to do fluids dynamics simulation. I use t=0.001s as the time step. But I don´t know how many iterations I need to achieve velocity ...
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0answers
195 views

How to estimate if a velocity field is statistically homogeneous?

For a 3D velocity field $\mathbf{u}$ obtained by direct numerical simulation. Assuming that the field is defined on a periodic domain $\mathcal{P}$ of periodicity $L_x$ in the $x$ direction, $L_y$ ...
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3answers
2k views

Finite-size effects in molecular dynamics simulation

I will be blunt: this is an old exam question of a course that covers Molecular Dynamics (MD) and Monte Carlo (MC) simulations. Explain how to determine the severity of finite-size effects. My ...
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1answer
173 views

Use of random numbers in the Metropolis algorithm

In the Metropolis algorithm, we accept or reject based on following criterion in the $NVT$ ensemble: $$ e^ {(E_{\text{new}} - E_{\text{old}})\,/ \,kT } \ge \text{random}(0,1). $$ Why does the ...
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0answers
55 views

Energy anomolies in many body simulation

I am trying to simulate the gravitational interaction between many bodies. I am using a direct PP force calculation and a 4th order symplectic integrator with a variable step size. The energy of ...
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1answer
74 views

Counting valency of atoms, in a molecule with python

The documentation for the indigo module can be found here http://ggasoftware.com/opensource/indigo/api#inputoutput So for instance if I have a molecule object for some SMILES string, e.g. ...
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1answer
175 views

Stabilization of solution to one-dimensional system of PDE

I am trying to solve numerically next PDE system: $$\frac{\partial c}{\partial t}=\epsilon\frac{\partial}{\partial x}(\frac{\partial c}{\partial x}+\rho\frac{\partial \varphi}{\partial x}+\frac{vc}{1-...
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1answer
4k views

How to do co-simulation with two FMU models

I have two FMU developed with different simulation tools. I would like to connect them through some variables and run a co-simulation with an open source tool as OpenModelica. This co-simulation has ...
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5answers
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Finding the correct Molecular Dynamics library

I just started working on some Biophysics research, and I was looking around for a good MD library to use. There is one right now at the university set up in C, with openMC parallelization, but the ...
3
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1answer
97 views

Simulating evolution of comet

I have to present a working 3D simulation of an arbitrary comet in a close proximity to the Sun or to the Jupiter. In specific, I want to simulate comets D/1993 F2 and C/2011 W3, using the theoretical ...
3
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1answer
193 views

Is using Monte Carlo method a good approach for solving Boltzmann equation?

I'm trying to solve for electron and hole distribution function using Boltzmann equation with various scattering mechanisms. Since I land up with an integro-differential equation, analytical solution ...
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2answers
829 views

Simulating laminar fluid flow in microfluidics device

I just started working in a lab that is trying to design microfluidics devices to trap and manipulate colonies of E. coli cells. Given a 3D model of such a device created in Autodesk Inventor (or a ...
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1answer
419 views

Verlet Leap-frog Method of approximating orbits

I found the following simulation of an orbit given the semi-major axis of the ellipse, eccentricity, initial velocity, the mass of the object being orbited, and initial position of the orbiting ...
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1answer
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How to evaluate 1st and 2nd order reactions, with rate constants and fluxes?

I want to implement differential equations in C# from Open Cell cellml file. The mathematical model is described in this article. I have parsed xml, and calculate operations, but can't correctly ...
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4answers
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Is CFD used in animations / movies / art?

This is not a technical question, and is asked just out of curiosity. Are computational fluid dynamics (CFD) simulations used in animation movies? (something like shallow water equations, explosion ...
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1answer
145 views

Spring damper model does not work very well

I'm trying to model a spring damper system from a tutorial that I've found on this site. If I use the exact same parameters as the ones in the tutorial the system is not stable. I've downloaded the ...
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2answers
184 views

Earth and Moon computer simulation

Edit: I made a test model with 2 bodies. The sun and earth or w/e. But I now have the problem of zero divisions every time that one of the coordinates is zero. ...
5
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1answer
854 views

Package for determining power output of windmill shapes?

I'm looking for the best package for doing the following: building a 3D model (or loading externally) of a non-standard windmill shape, simulating an airflow over the model, and determining the ...
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2answers
151 views

How does longer simulation time affect simulation results?

I have a transient flow and solute transport simulation running using a fortran code. The final solution time is 1 day. I need the output of hydraulic head for the output time of 0.5 day. I want to ...
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2answers
3k views

C++ alternatives for simulating dynamic systems

I'm looking for alternatives to Matlab/Simulink and Dymola for simulating a non-linear dynamic system. I know it's possible to implement the time-domain behavior without a lot of code and a good ...
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0answers
507 views

How does GAMG in OpenFOAM really work?

I use OpenFOAM for CFD simulations. A very popular preconditioner is GAMG which needs a low number of iterations per a time step in SIMPLE or PISO solvers that are used to simulate the fluid flow. I ...
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
1k views

Boundary conditions in fluid simulation

I'm working on a 2D fluid sim using vortex particles/"vortons" as described in Fluid Simulation for Video Games. Which I think is the same things as the "discrete vortex method". Basically you ...
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2answers
530 views

Numerical simulation of particle in magnetic field

I'm interesting in numerically simulating (with my own code, not an off-the-shelf package) the motion of a single electrically charged particle in a magnetic field. The field will vary in time and ...
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3answers
213 views

Is there a way to reduce aberration in computations of planets' trajectories?

I don't think the title is very accurate , sorry for that. I simulate bodies in space using two timestep: the TIMESTEP is the Δt wich I use to make the calculation and XTIME is the number of times ...
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2answers
758 views

How to solve the stiff equation in this Restricted Three Body Problem numerically?

I've come across a stiff equation in solving the Circular Restricted Three Body Problem. [An object is moving considering the effect of the gravitational forces caused by two gravitational sources ...
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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, ...
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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-...
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4answers
400 views

Arbitrary Accuracy Scalable Rope Simulation

I am trying to simulate a rope object. The formulation I understand is an array of particles, connected by springs. These springs have very large k-values, so that the line deforms, but stretches ...
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4answers
2k views

Fourier pseudo-spectral method and numerical dissipation

Performing a direct numerical simulation of isotropic turbulence with Fourier pseudo-spectral method (Orzag & Patterson, PRL, 1972) using FFT. For a background of the method, which is widely used ...
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1answer
213 views

How are collisions detected in simulations?

I want to understand how does the simulation identifies and models when two bodies are colliding with each other. For example car crash simulation. The car moves towards the wall or another crash. ...
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3answers
784 views

Maximizing unknown noisy function

I'm interested in maximizing a function $f(\mathbf \theta)$, where $\theta \in \mathbb R^p$. The problem is that I don't know the analytic form of the function, or of its derivatives. The only thing ...
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1answer
136 views

How to add perturbation to a base state in physical grid space?

For study 3D instabilities problem i.e a base state (velocity field and temperature field) and an additional perturbation. The method must be independent of the type of instabilities considered but ...
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3answers
231 views

How to estimate the impact of small scale on large scale in fluid dynamics?

Assuming that a direct numerical simulation is performed, what is a good method for estimate the impact of small scale on large scale in fluid dynamics ? For example is it pertinent to compare two run ...
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1answer
751 views

What is the scaling or order of molecular dynamics (MD) simulations?

Often in computational science, we talk about the scaling or order of a particular method ($\mathcal{O}(N)$, $\mathcal{O}(N^2)$, $\mathcal{O}(N \log N)$, etc.). I am having a really difficult time ...
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78 views

Can similarity criterion help reducing calculations in Finite Element Analysis (FEA) problems?

Can similarity criterion help reducing calculations in Finite Element Analysis (FEA) problems? I'm using NX (a thermal and CFD simulation software) to simulate the temperature and fluid field of a ...
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2answers
1k views

Monte Carlo simulation of 3D X-Y model

I need to compute the helicity modulus as a function of temperature for a three-dimensional X-Y model (see N.K. Kultanov, Yu.E. Lozovik, "The critical behavior of the 3D X-Y model and its relation ...
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1answer
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How to find Lyapunov exponent for coupled system

Answer gives a software for calculating conditional Lyapunov exponent (CLE) for coupled oscillators in chaos synchronization. However, it is hard to follow and there is no graphical output of the ...
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3answers
785 views

How to handle large numbers of output data sets from a simulation/sensitivity analysis?

Somewhat related, but I think the question is distinct enough to justify a separate question. As a bit of background, I come from a observational/statistical Epidemiology background, working with ...
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5answers
2k views

Parallel Scientific Computation Software Development Language?

I want to develop a parallel scientific computation software from scratch. I want some thoughts on which language to start. The program involves reading/writing data to txt files and doing heavy ...
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3answers
6k views

What are the advantages and disadvantages of the particle decomposition and domain decomposition parallelization algorithms?

I am running molecular dynamics (MD) simulations using several software packages, like Gromacs and DL_POLY. Gromacs now supports both the particle decomposition and domain decomposition algorithms. ...
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2answers
112 views

Are there any QM macromolecule simulation methods that can use an electron density map as input?

I am not an xray crystallographer, but from what I've heard there's often a good deal of guess work and intuition involved in the process of fitting a ball-and-stick molecular model to a crystal-...
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7answers
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Where do the laws of quantum mechanics break down in simulations?

As someone who holds a BA in physics I was somewhat scandalized when I began working with molecular simulations. It was a bit of a shock to discover that even the most detailed and computationally ...
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2answers
262 views

Representing charges in computer programming

I'm preparing for a thesis in computer science on calculations based on concepts from Neuroelectrodynamics. In short this theory states, that information transfer is not done by spike time coding, ...