Questions tagged [simulation]
Simulation is the process of mimicking the behaviour of a real physical process or system using a representative model.
196
questions
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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 ...
1
vote
0answers
45 views
Using MATLAB to simulate the Ising Model
I am using MATLAB to simulate a 1D Ising Chain. I am running into an issue where when trying to find heat capacity, my system has a tremendous amount of noise. I'll post my code and an image of the ...
-1
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1answer
42 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 (...
11
votes
2answers
391 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
votes
1answer
57 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 ...
2
votes
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 ...
3
votes
1answer
81 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 ...
0
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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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0answers
36 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
votes
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:
...
2
votes
1answer
62 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 ...
0
votes
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. ...
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
votes
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
votes
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
vote
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
vote
1answer
125 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
vote
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 ...
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
57 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$$ where $p$ is the probability of finding molecules in the 3-D environment. I want to ...
3
votes
1answer
58 views
Radiation heat transfer between surfaces
I'm trying to model the temperature distribution over a curved surface. Apart from the heat equation, I need to take into account the energy emission/absorption through electromagnetic radiation. The ...
-1
votes
1answer
64 views
Writing parallel code for molecular computation [duplicate]
I recently moved towards computational biophysics from an experimental science background. As of now, I am learning the fundamentals and doing some basic monte carlo simulations of LJ fluid on my ...
1
vote
2answers
87 views
Custom exponents for Lennard Jones in LAMMPS
I am trying to run an MD simulation using this generalized version of Lennard Jones.
$$
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 ...
3
votes
2answers
499 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 ...
1
vote
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
votes
0answers
93 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
votes
1answer
92 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
votes
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
votes
2answers
137 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
117 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
votes
2answers
424 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 ...
2
votes
1answer
293 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 ...
1
vote
2answers
2k 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/...
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0answers
48 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 ...
4
votes
2answers
216 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 ...
2
votes
0answers
158 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).
...
0
votes
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, ...
4
votes
1answer
96 views
Finite-volume method applied to a particular advection equation
I'm trying to apply the finite-volume method (FVM), with which I'm not so familiar, so a simple 1D PDE equation. I already asked this question in the math stackexchange, but was told that it could be ...
1
vote
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 ...
1
vote
2answers
158 views
Discussing the energy spectrum of Langevin Dynamics simulation of many atoms
UPDATED
I've coded a multiparticle MD simulation in 3D. It is based on Langevin Dynamics, with random impulse and dissipation. I think the program works correctly now? I have attached the plots of ...
0
votes
1answer
101 views
Sampling simulation steps logarithmically
The common case of for instance a Monte Carlo simulation is, if we want to run our simulation for $N$ steps, we define a delta $\Delta,$ such that $N/\Delta = n$ tells us the frequency with which we ...
3
votes
1answer
118 views
Diffusion properties of hard spheres in Monte Carlo simulation
In standard Monte Carlo simulations, say for hard sphere systems, how should one compute the mean-squared displacement of the spheres in order to extract dynamical properties such as the diffusion ...
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0answers
59 views
Dealing with simultaneous collisions in N-body sim
I have written an 2d N-body simulation in Python which allows collisions between the bodies.
A body is modeled as a circle whose area is proportional to its mass. Each time the sim advances by one ...
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0answers
19 views
Does excitation type matter in a time-domain simulation/computation of a transfer function of an LTI system?
Let's say I am running a FDTD simulation of a wave-equation to determine a transfer function of an LTI system:
\begin{equation}
H(f) = \dfrac{Y(f)}{X(f)}\
\end{equation}
where $Y(f)$ and $X(f)$ are ...
1
vote
1answer
89 views
Oil/Water interface simulation using GROMACS
I would like to perform a decane/water(tip4p) interface simulation using GROMACS to analyse the fluctuation of the interface over a long period of time (50ps - 1ns).
Though I have a rough idea on ...
1
vote
1answer
67 views
Why can we predict global temperatures years ahead but we cannot reliably predict weather weeks ahead?
In case of global temperatures we are interested in aggregate values rather than local distributions. Is this the reason we can accurately predict one but not the other?
