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

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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 ...
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2answers
84 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 ...
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13 views

How to do numerical simulation of Impulsive Differential system?

I am working on a research paper on Plant-Pest-Natural enemy model. I want to plot graphs for my system as given below. I know how to simulate differential system using ODE45 command and then using ...
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105 views

Relationship between FEM solutions of PDE with different spatial resolutions

I use FEM to simulate deformations of elastic objects for animation applications in computer graphics. The governing equation is generally with the form: $$ \mathbf{M}\ddot{\mathbf{u}} ...
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31 views

modify COMSOL codes

I am a physics student and I am planning to simulate microfluidics and capillary waves on a fluid film and I decided to use COMSOL. I am not so much aware of COMSOL abilities. I wonder if I can ...
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36 views

Conservation at grid interface in adaptive mesh refinement

I am using adaptive mesh refinement to solve one dimensional inviscid Burgers equation. However I am facing some difficulty to handle grid interfaces which are not uniform (coarse-fine grid ...
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1answer
95 views

GPU-enabled Lattice Boltzman solvers?

Is anybody aware of any GPU-enabled Lattice Boltzman solvers (preferably on C++/OpenCL and open-source) that would be recommended? I have found Advanced Simulation Library, but it seems to be very ...
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1answer
32 views

How to generate movie of the simulation done in LAMMPS? [closed]

I simulated nanowire deformation using LAMMPS and visualized it using VMD in Centos 6.5. But I'm not able to generate .jpg image file or the simulation movie. How can I proceed??
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49 views

How come in distributed computing 10X 32GB systems doesn't equal 1 320GB system

is there a mathematical formula to relate how much memory per node is lost when you use parallel computing? for example, when running COMSOL (FEA, MUMPS) in parallel, a problem that would require ...
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78 views

Should a colorbar have constant values throughout a simulation?

The default option for matplotlib's pcolormesh (also true for VisIt and I think also true for Matlab) is to allow the maximum and minimum of a colorbar vary. Which ...
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45 views

Modelling a Quantum Cascade Laser (QCL - GaAs atop Copper Heat Sink) with COMSOL

I am trying to model this: GaAs on-top of a heat-sink made of Copper. It's trying to simulate a type of Quantum Cascade Laser, I'm looking at the effect the temperature has by running a 10 V ...
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1answer
82 views

Hypersonic flow in Fluent

I am working in my graduating project about the hypersonic flow, particularly the properties of the air behind a strong shock wave, I try to do a simulation for that process in Fluent but I don't know ...
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27 views

Book recommendation on simulation of linear and nonlinear electronic circuits

I am looking for a book on electronic circuit simulation explaining the numerical modeling using transient and frequency based methods from a computational point of view. It should also have an ...
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2answers
90 views

Simulating a Simple Pendulum - Increasing amplitude on each swing?

I am trying to animate a dampened pendulum using RK4 for a highschool project. The equations that describe the dampened system are as follows: (from ...
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1answer
83 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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2answers
102 views

How to interpret/convert density in 2D simulations?

Density has units of $kg/m^3$. In simulations often scaling is done to deal with non-dimensional values, so the physical density is converted to the non-dimensional density so that it can be used in ...
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1answer
45 views

Value of density when there are no or very few neighbours in SPH simulation

Sorry for the noob question. I am trying to implement SPH using the directions shown in this paper. The density needs to be updated using the formula The smoothing kernel is If there are no ...
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56 views

Is there an opensource aircraft boarding simulator?

A friend and myself think that we have developed a method to speed up the boarding process of large aircraft. After doing a quick patent research we think about launching a start-up. Before doing so ...
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71 views

Tracking the speed of 2D oscillations on a lattice

I wrote a Monte Carlo simulation of the 2D Lotka-Volterra model on a discrete lattice (with periodic boundary conditions). A video that I produced (which images the system after some number of monte ...
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51 views

Is it normal to expect the error of simulation of a damped harmonic oscillator to decrease as the damping factor decreases?

I am simulating a damped harmonic oscillator using the RK4 method of numerical integration. I am comparing the simulated results with the analytical ones (for the free evolution case) and obtaining ...
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33 views

Parameter estimation with RNetLogo : chosing estimation technique with both continuous and discrete parameters

I want to estimate parameters for an agent-based model in Netlogo using R and the RNetLogo ...
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1answer
105 views

Poisson solver diverged

My 2D-Poisson solver is build for simulation of semiconductor. The algorithm is Gauss-Seidel iterative method. If I use simple PN junction for simulation testing, it diverged while I applied high ...
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3answers
396 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 ...
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227 views

Using Trilinos and/or Petsc in Windows with Visual Studio?

I am currently working on a project of building a simulator. Up till now I have mostly played around with very simple examples, but with regards to the future I have been thinking that it might be a ...
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1answer
92 views

Confusion in modeling and computing [closed]

I come from a computer graphics background without any professional in computational science. But I find my job(game engine development) being related to this field. May I ask some general questions ...
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1answer
258 views

Numerically solve a PDE in Python with a term calculated by coarse-graining

I'm trying to solve a PDE in Python of the form, $\dfrac{\partial c(\mathbf{x}, t)}{\partial t} = \mathrm{D} \nabla^2 c(\mathbf{x}, t) -\gamma \rho(\mathbf{x}, t) c(\mathbf{x}, t)$ where $c$ ...
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What are the specific generic properties do Ansys consider while running a Non Linear Analysis?

When Working on Ansys Non Linear Static Structural Analysis, I couldn't comprehend while defining and assigning material properties to corresponding bodies. When I give different random values for ...
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2answers
87 views

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 ...
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1answer
168 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
171 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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1answer
57 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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25 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 ...
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1answer
215 views

PyOpenGL/OpenGL Generating Cosmic NBodys

I am working on a Universe Simulator. I'm stuck on creating the dark matters webs of the universe that look like this: http://www.mpa-garching.mpg.de/galform/data_vis/sim3dnew-highres.png I am ...
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228 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
319 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
137 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 ...
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4answers
154 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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51 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
109 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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2answers
321 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
158 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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48 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 ...
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1answer
234 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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3answers
263 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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1answer
289 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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84 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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1answer
71 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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1answer
140 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
105 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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Generating magnetic turbulence spectrum

I am trying to code up a model of magnetostatic turbulence and am having issues with the build. The paper that I am referring to is titled "Anomalous diffusion and Lévy random walk of magnetic field ...