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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Simulating interaction of Smart Fluids with Solids

Is it possible to simulate interaction of Smart Fluids with Solids? Is there a software capable of doing so? What I Know: The two software that I know of are Autodesk Simulation Mechanical and ...
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 ...
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2answers
226 views

Which processor should I consider buying for a desktop built for scientific computing?

I run Python/C simulations for biological problems, so the range of computational tasks can be broad. Here are some examples: 1) continuum model simulations: FEM type 2) agent-based simulations: ...
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437 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 ...
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1answer
177 views

Is it possible to simulate fluid dynamics in a time-based and deterministic manner?

The Problem Domain I have a number of network-connected PCs. I want to be able to simulate and replicate the same simple fluid dynamics simulation (E.g. Navier-Stokes), in real-time, between them. ...
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1answer
61 views

Iteratively refine bounds on exp for Metropolis criterion

In Monte Carlo simulations, using the Metropolis criterion, one often has to compare a random number $a$, $0 \leq a < 1$, to the Boltzmann distribution $exp(-\beta\Delta E)$, where $\Delta E$ is ...
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2answers
438 views

How can I create a computational model of the human eye?

I need to create a program that can simulate the optical system of the human eye. The input will be any image, the output would be the image that is projected onto the retina. I need it to be as ...
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3answers
1k views

Implementation of Navier-Stokes Equation for Ocean Waves

I am doing an undergraduate research to model ocean waves in shallow waters in real time. I am trying to base my research on Navier-Stokes equations since they produce the most accurate mathematical ...
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4answers
179 views

What scale problem can be simulated on an PC using Smooth Particle Hydrodynamics?

I want to simulate tidal features in a large body of water using was smooth particle hydrodynamics. For a system composed of an incompressible fluid, what general scale of problem can be tackled with ...
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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. ...
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1answer
98 views

Barnes-Hut algorithm and recursion limit

If while distributing particles to their corresponding nodes, two particles comes closer to a level smaller than the machine precision (or $\Delta d \to 0$), how is the situation to be treated? Should ...
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0answers
147 views

Algorithms for adding hydrogens on a molecule

I want to add hydrogens to some linear polymer molecules (polyethylenes). I know some working methods like using PyMOL internal function h_add. This method works, but hydrogens are added at distances ...
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1answer
1k views

Celestial mechanics simulation software? The 'N-Body Problem'

What software or sites might simulate an N-body gravitational problem? Application is related to Klemperer Rosette or Iridium Satellites. Bias for C, C++, PHP, or Java. Nice visuals a big plus. ...
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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 ...
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1answer
1k views

Euler's equations for a tube with varying cross-section

$\def\pd{\partial}$ $\def\l{\left}\def\r{\right}$ $\def\mdot{{\dot{m}}}$ $\def\eps{\varepsilon}$ Consider a tube with longitudinal coordinate $x$ from $0$ to $l$ and varying cross-section $A(x)$. ...
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55 views

Discretizing boundary conditions for vortex methods

I am working on a fluid simulation using vortex methods. For this I must compute the vortex sheet on my boundaries given as: $$ \gamma(\mathbf{x}) - \frac{1}{\pi}\int_S \frac{\partial}{\partial\mathbf{...
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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 ...
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100 views

Tracking for two meshes

I'm dealing with physical simulation (position based dynamic). Now I'm trying to realize tracking for two meshes. In order to explain what does it mean, let's assume that we have two similar meshes: ...
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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 ...
4
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1answer
517 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 ...
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2answers
196 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 ...
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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 ...
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0answers
54 views

Calculating the number of molecules diffusing out of a volume [closed]

I have a system of reactions that are governed by differential equations. They are reacting inside of a volume with known dimensions i.e lbh. I don't have any other information on their position ...
2
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1answer
991 views

Particle Tracking Code - MATLAB vs. C++

First some background, I am a mathematician by training with very little formal training in programming. I am most comfortable in MATLAB and have been working with it for a long time. My second choice ...
2
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1answer
116 views

Detect rigid body motions in a cloud of points

This question popped up today in our group meeting. Suppose you are given a cloud of N points in 2D and each is associated with a velocity vector. These points are associated with particles on a 2D ...
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0answers
241 views

N-body simulation for particles

I would like use N-body simulation for measure a torque on an object in a liquid (helium). It's a 2D study. On the site : http://www.browndeertechnology.com/docs/BDT_OpenCL_Tutorial_NBody-rev3.html I ...
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0answers
235 views

Sound Waves Simulation in 3D Environment

I want to do a simulation of sound waves including wave propagation, absorption, and reflection in 3D space. I did some research and I found this question in stackoverflow but it talks about ...
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2answers
919 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-...
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0answers
174 views

How can i find the coordination number with voro++? [closed]

Could anybody please help with voro++ cause i am new to this software?My problem is how can i find the coordination number of an atom ,cause i checked it for a bcc lattice and it gave me 24 for all ...
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1answer
231 views

Non-deterministic/probabilistic molecular dynamics simulations

I'm looking for a piece of software for performing molecular dynamics simulations with the following specifications: required: well published (as in there are papers citing it in one or more ...
3
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1answer
88 views

numerical inaccuracy ellipsoid-ellipsoid collision

I am trying to implement ellipsoid-ellipsoid collision in my C++ code. Briefly this task can described as next: Let's assume that we have two arbitrarily oriented ellipses in the in space and this ...
4
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0answers
113 views

What are the governing equations solved in coupled atmosphere-ocean models?

In (hydrostatic) atmospheric general circulation models, for example the so-calle Primitive Equations, consisting of the horizontal momentum equation, the hydrostatic balance, the continuity equation, ...
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1answer
140 views

Simulating the motion of a elastic body under gravity [closed]

I am doing a numerical simulation of a elasticity problem. It is very simple. A cuboid elastic body with the right end fixed on the wall, under the gravity(but here I set it to be 1 along the z-axis ...
3
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4answers
571 views

Finding a molecular dynamics visualization library for C

I asked this question over at stackoverflow, and got blasted for it. I am currently working with legacy MD code written in C that my university uses, and haven't moved to a more modern library like ...
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1answer
169 views

Simulate aerodynamics of a general shape object

I'm trying to code a simple physics simulator in C++ but I'm stuck on the air resistance issue. Surfing the Internet I only find a drag coefficient for very basical area shapes when the air is ...
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0answers
41 views

Spectra of the energy flux VS transfer spectra?

In direct numerical simulation of turbulence what is the advantage to look at the spectra of the energy flux rather than the transfer spectra? The transfer spectra corresponds to the triple-velocity ...
0
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1answer
142 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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85 views

References on the topic of DEM and XDEM

DEM: discrete element method. XDEM: extended discrete element method. For my current project of furnace simulation with granular materials, I am interested in the methods mentioned above. I have not ...
3
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0answers
209 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, $L_y$ ...
3
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1answer
184 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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1answer
78 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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0answers
57 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 ...
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-...
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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 ...
3
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1answer
99 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
214 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 ...
4
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1answer
433 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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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, ...
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1answer
65 views

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 ...
3
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2answers
191 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. ...