Computational Science

Questions tagged [simulation]

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

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30
votes
7answers
2k views

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 ...
19
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5answers
3k 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 ...
15
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3answers
7k 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. ...
14
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1answer
1k views

Conserving Energy in Physics Simulation with imperfect Numerical Solver

I am creating a C++ Physics Simulation where I need to move an rigid body through an acting force field. Problem: simulation does not conserve energy. Quesiton: abstractly, how is conservation of ...
12
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2answers
422 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 ...
12
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4answers
436 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 ...
10
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3answers
832 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 ...
10
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3answers
2k views

What are the differences between CFD simulations and realistic ocean/atmosphere model simulations?

The field of computational fluid dynamics (CFD) is dedicated to solving the Navier-Stokes equations (or some simplification of them). A subset of CFD, ocean and atmospheric models numerically solve ...
10
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2answers
436 views

Why do the shape of finite elements matter?

I have used FEA for a couple of years now, but using it and using it correctly are two different things, safety factor is not the solution to everything. I have the feeling I won't be using it right ...
10
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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". ...
9
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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 ...
9
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1answer
2k views

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 ...
8
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4answers
2k views

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 ...
8
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5answers
985 views

Is Discrete Exterior Calculus currently a focusing point in numerial computing world or simulation in industry,

I am just wondering if Discrete Exterior Calculus, as a new numerical method , is good at numericall solving problems in elasticity, fluids or other physical/real area.
8
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3answers
237 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 ...
8
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2answers
817 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 ...
8
votes
1answer
204 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 ...
8
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1answer
188 views

Efficient Gravitational Field Implementation

I asked a similar question on physics.stackexchange, being ignorant about this website. I am basically looking for an efficient way to implement gravitational fields. I have a huge 2D space, with ...
7
votes
4answers
196 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 ...
7
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2answers
263 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, ...
7
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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 ...
7
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2answers
913 views

Feasibility and software for acoustic simulation

I'm looking at doing a finite-element simulation of air flow essentially for the purposes of approximating the response to an external audio impulse of a smallish (~10-30 cm scale), stationary 3D-...
7
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3answers
805 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 ...
6
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1answer
253 views

What kind of a researcher am I?

So far, I've worked a bit in modeling, simulations and simple lab experiments, and I've really enjoyed all three research methods to approach a single research question. I can write tricky (in terms ...
6
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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 ...
6
votes
2answers
536 views

Simulating advection over a network of 1D pipes

I am trying to create a simulation to help visualize how different chemical components flow through a network of pipes with associated valves, pumps, and chemical inputs. In this simulation, the pipes ...
6
votes
2answers
381 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 ...
6
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1answer
379 views

Lagrange Multipliers in Multi-body Finite Element Code

I'm working on a Multibody dynamics code using the finite element method to simulate the behaviour of flexible beams (using this paper if anyone is interested/ it is relevant). I'd like to model ...
6
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0answers
123 views

Is a complete bacteria simulation with an exascale supercomputer possible?

Will it be possible to simulate a complete (at least simple) bacteria atom by atom on an exascale supercomputer? or is it possible already today with the largest systems? Here, I've read that ...
5
votes
3answers
215 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 ...
5
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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 ...
5
votes
1answer
848 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 ...
5
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2answers
122 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 "...
5
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3answers
888 views

What do C, C++ and Java have that Fortran 2003 don't? [closed]

As you may know, Fortran is widely and longly (?) used in science. I've heard a lot of people saying that we natural scientists should all migrate to C++ or Java. I've seen people increasingly ...
5
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1answer
874 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 ...
5
votes
3answers
2k views

Monte Carlo estimation of Pi with Buffon's needle

Is there a way of estimating Pi with the Buffon's method without assuming Pi known? To be more precise: in a Monte Carlo simulation of the experiment invented by Buffon I would (ideally) generate 2 ...
5
votes
1answer
448 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-...
5
votes
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-...
5
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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-...
5
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0answers
109 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 ...
5
votes
0answers
893 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 ...
4
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2answers
249 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 ...
4
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5answers
2k views

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 ...
4
votes
2answers
119 views

Can other running processes harm the performance of my simulation?

I don't have an high-end machine on which run my simulation (Python + C extensions, based on numpy for calculations) Thus I intend to run the program on my PC, for several hours. I won't use the ...
4
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2answers
563 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 ...
4
votes
2answers
152 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 ...
4
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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 ...
4
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1answer
514 views

Increasing thread number degrades performance

I have a problem with parallelization and the brownian dynamics (molecular dynamics) code that I am using. We have our own home-grown framework at the university, and recently we've made the change ...
4
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2answers
194 views

Solving system of differential equations with interconnected boundary conditions

I am trying to solve the following system of differential equations numerically over the domain $x=0$ to $x=D$. The main difficulty is that the boundary conditions are interconnected and depend on the ...
4
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1answer
439 views

Surface charge boundary conditon for Poisson-Boltzmann solver

I want to set up a surface charge boundary condition for the simulation of semiconductor and electrolyte interface. The 2D-Poisson example and surface charge boundary condition are shown in following ...

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