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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1answer
28 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?
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1answer
41 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 ...
1
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1answer
33 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 ...
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1answer
51 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
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1answer
33 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
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2answers
88 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
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1answer
74 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
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0answers
72 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
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1answer
186 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 ...
-1
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1answer
74 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?
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0answers
34 views
Stochastic simulation Gillespie algorithm for areas instead of volumes?
I am trying to find resources on the Gillespie stochastic simulation algorithm for my system which happens on a surface. The original algorithm was developed for a reactor of volume $V$, but my system ...
1
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1answer
39 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 ...
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1answer
48 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 ...
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2answers
78 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
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1answer
75 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 ...
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2answers
115 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 ...
3
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1answer
69 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 ...
0
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2answers
516 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/...
1
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0answers
32 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 ...
5
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2answers
145 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
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0answers
84 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
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1answer
58 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, ...
5
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1answer
85 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
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1answer
90 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
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2answers
142 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 ...
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1answer
96 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 ...
4
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1answer
100 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 ...
1
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0answers
49 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 ...
1
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0answers
17 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
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1answer
70 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
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1answer
64 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?
1
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0answers
37 views
Simulating periodic boundary condition with long_range interaction
Consider 2 particles in a 2D plane. There is a long-range interaction between two particles:
$$f (r_i-r_j)= \frac{\vec{r_i} - \vec{r_j}}{|r_i-r_j|^3}$$
$$\vec{r_i} =(x_i,y_i)$$
$r_i$ determines the ...
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1answer
54 views
Applying pressure on simulation box
We have a 3D simulation box (cubic, side $L$) filled with $N$ non-overlapping objects (say spheres). We are interested to study the evolution of the system under an applied pressure in the z-direction ...
0
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1answer
73 views
Questions about implementing an electromagnetism/photonics solver package
I am hoping to start (very slowly) on implementing some form of a computational photonics/electromagnetism package. I know things like Meep, S4, FDTD++, EMPy, and a host of other proprietary/free/...
1
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3answers
296 views
2D simulation of a particle with different diffusion coefficient in different directions of the particle
How can one simulate diffusion of a particle which has a natural axis and diffusion coefficient of the particle in the direction of the axis is D_1 and in perpendicular to the axis is D_2?
Could ...
0
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1answer
70 views
Multiscale Simulation of random walker
I want to simulate a system of random walkers (called A) with diffusion coefficient equal to D and other systems of random walkers (called type B) with diffusion coefficient equal to 1000 D. Second ...
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2answers
89 views
A program to simulate cellular automaton model
I have worked on mathematical modeling based on differential equations, and now I want to simulate a cellular automaton based on a ...
1
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1answer
129 views
How do I simulate an open end?
When simulating a partial differential equation describing a physical phenomenon like vibrations on a string, fluid flow in a chamber or quantum wave functions, the most straight-forward way is to ...
1
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1answer
95 views
GAMS Optimization
I am writing a GAMS program where I am interested in using the value of a variable as a condition inside an another equation. Let's say I have two equations with two variables, $g_1(t)$ and $g_2(t)$, ...
1
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2answers
71 views
Should energy be conserved in an N-body simulation where particles don't lose energy in collisions?
In an N-body simulation where forces between particles are attractive and particles do not lose energy on colliding with walls or each other, should energy be conserved? How could it be, with total ...
1
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0answers
205 views
Simulating a Hill-Type muscle model
I'm trying to do biologically based locomotion animation.
I have a Hill-Type Muscle Model (see reference 1) that I've implemented in code. I can find the initial lengths of the tendons, then do a ...
0
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0answers
134 views
Speed up matrix calculation in R
I'm simulating in R a Geometric Brownian Motion, for different correlated companies (nComp), and number of days (nDays). Wt are the the correlated Brownian paths.
I'm running the following code, for ...
1
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0answers
60 views
Dielectric in an external electric field
I want to numerically solve for electric field of an object in an external electric field. The object has linear displacement field such that its permitivity ($\epsilon$) is constant. The object's ...
0
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1answer
96 views
Infinite force in simulation [closed]
In physical problems the infinite force is easily implemented by the mathematical form of that force, take $1/r$ as an example, whenever the distance between two particles becomes small the force goes ...
1
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0answers
53 views
RCWA for Non-Periodic Structure?
I have a quick question regarding Rigorous Coupled Wave Analysis (RCWA) for numerically solving problems (in optics). I am trying to simulate a device which is non-periodic in x, y directions (but is ...
2
votes
0answers
181 views
Error in MD simulation with Lennard-Jones potential in C, resulting in a lack of conservation of energy
I'm working on a MD simulation using the Lennard-Jones potential and the Velocity Verlet algorithm. The code compiles and runs, but the energy for each time step is not conserved; it decreases ...
2
votes
1answer
111 views
How does Multi Body Dynamics software work for flexible joints?
I need to model a "fishing rod" in 2 dimensions by joining several "rigid sticks" by flexible/elastic joints. The joints act as plate/torsion springs with different spring constants. The "fishing rod" ...
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1answer
317 views
Three body problem in C++
I am in a begginers programming course and we got a little project. I chose to simulate the three body problem using the Euler method. Even though the system is chaotic there are some special cases ...
3
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0answers
146 views
Initial conditions of nbody problem
Note: I have edited the original question to try to be clearer.
I'm trying to simulate a gravitational nbody problem with a Barnes-Hut algorithm, in which the bodies start in a homogeneous sphere ...
1
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1answer
76 views
Convergence Criteria for Two Fluid Flow Solver
Which one of the following is suitable for judging convergence in Two-Fluid Flow Solver?
1) Absolute Residual (L^2-Norm).
2) Relative Residual.
3) Fraction Change in Velocity, Pressure and Volume ...
