# Tag Info

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### Conserving Energy in Physics Simulation with imperfect Numerical Solver

There are a few ways to conserve energy during ODE integration. Method 1: Symplectic Integration The cheapest way that is to use a symplectic integrator. A symplectic integrator solves the ODE on a ...

### What guidelines should I follow for simulation software projects?

I maintain (and am the main coder of) a simulation software that has been developed for ~8 years and is used by few hundreds people. It all started as a side project during my PhD, and it clearly ...
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### What guidelines should I follow for simulation software projects?

"developers lack the skills". Maybe. I think it's much more likely that the developers lack the incentives. Making solid code is difficult and expensive and, in academia, comes with minimal-to-...
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### How do I simulate an open end?

The problem you describe, how to prescribe non-reflecting or absorbing boundary conditions when solving partial differential equations (PDE) has been extensively studied. For complex (e.g. nonlinear) ...

### Why not use the convolution theorem for explicit timestepping?

This is a linear PDE, and so while this technique works here, it would not work for any nonlinear PDE. Often times when people are solving these equations it is to get experience with common solution ...

### Methods for solving $x'=Ax+b$ for small, sparse, singular $A$

Any general-purpose ODE solver should be able to handle this linear coupled system of ODE very easily, for example: scipy.integrate.ode CVODE from the Sundials solver suite; it appears to have Python ...

### Optimization techniques for expensive multi-variable functions

One commonly used approach is the "Response Surface Method" in which you sample the feasible region, running the full simulation at the sample points, then use regression techniques to fit a surrogate ...
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### What kind of a researcher am I?

Up until a couple of decades ago, science was based on two large pillars. Those were theory and actual physical experiments. It is an exciting time to see a third pillar arise with numerical ...

### Maximizing unknown noisy function

There are several Bayesian optimization techniques you could try. Easiest are based on Gaussian process: Harold J. Kushner. A new method of locating the maximum of an arbitrary multipeak curve in the ...

### Physics Simulation in C++

I think you are missing a very important and crucial step that lies exactly between the physics and simulation: the mathematical model. In order to model any physics, one has to formulate the ...

### Good desktop PC for molecular dynamics simulations

There is a recently published paper addressing the question of what is the optimal combination of hardware on which to run GROMACS: Kutzner, C., Páll, S., Fechner, M., Esztermann, A., de Groot, B. L.,...
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### Solve implicit ODE numerically in orbit simulation

(1) Using the previous value of $\ddot{r}_j$ is like adding an error term to the r.h.s. of your equation of magnitude $\mathit{const}\times(\ddot{r}_j(t+\delta t) - \ddot{r}_j(t))$, meaning your ...
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### MD Simulation: Reference for the Neighbor's List Method

I'd recommend "The Art of Molecular Dynamics Simulation" by D. C. Rapaport. The code samples are written in C. I'm not a huge fan of the programming style of the book, but at least it's not ...

### How to simulate over 1 billion particles?

A first step, if you "have never been up in computing", is to read the literature and see what others are doing and have done. The second step is that you will likely learn that what you want to do ...
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### Artificial Intelligence, Modeling and Simulation

So bottom line is I don't see any comprehensive work on the use of AI in M&S as a whole, let's say having models that can learn how to produce new improved models using the existing models. There'...

### Starting configuration for Molecular Dynamics

Usually one needs to employ periodic boundary conditions (at least in the horizontal directions). Any atoms which fly outside of the box will be mapped to the opposite side. This also has to be ...
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### Mean-squared displacement in Monte Carlo studies

This is possible (see ) but uncommon, as it requires Monte Carlo moves that alter the current conformations by a very small perturbation. In that setting of "small" Metropolis MC moves, it is ...

### Mean-squared displacement in Monte Carlo studies

It is in some cases possible to map the dynamics obtained in MC simulations to other (more realistic) dynamics, especially for the case of dense colloidal suspensions. The following two papers talk ...
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### Simulation-based Optimization vs PDE-constrained Optimization

Both approaches apply to the same problem (numerical minimization of functionals which involve the solution of a PDE, although both extend to a larger class of problems). The difficulty is that for ...

### What scientific problems can be simulated that couldn’t be simulated 10 years ago?

This report on exascale computing from the DOE might be useful: https://science.energy.gov/~/media/ascr/ascac/pdf/reports/Exascale_subcommittee_report.pdf
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### Can one publish a new model and simulation without physical experiments?

The short answer is: it depends. Some journals have a requirement or a guideline to have experimental results that corroborate the numerical simulations. For example, IEEE Transactions on Microwave ...
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### N-body problem with differents solvers (RK2, RK4, Euler symplectic, Stormer-Verlet) : planets drift to infinity

All-over this is a nicely structured code. The main problems are related to the Runge-Kutta solvers, where the first-order system was not uniformly applied to the computation. What is obviously wrong ...

### Why not use the convolution theorem for explicit timestepping?

For the linear, constant coefficient advection equation on a torus, one can simply use the exact solution. So there are no "popular" numerical methods for this problem.

### What evidence exists to suggest that computational science produces more information than studying real phenomena as they are?

This is the nature of science, at least the more physical ones. You have a hypothesis about some object. You devise some experiment that would highlight this hypothesis the clearest, with the least ...
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### Sorting eigenvalues by the dominant contribution

You'd like to sort eigenvalues/eigenvectors in a way that is continuous as you move through momentum. This highly constrains the sorting - for most k-points, you must sort the eigenvalues to be a ...

### Simple Simulation Examples in Computational Fluid Dynamics

There are many simple cases that you could look at, e.g. 2D-flow over a backward-facing step. Lid-driven cavity flow. (Inviscid) wave resistance of thin ships or travelling pressure distributions. ...
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### What do C, C++ and Java have that Fortran 2003 don't?

One thing that C++ includes that Fortran doesn't have is extensive support for generic programming and compile-time code ...
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### Is model-view-controller useful pattern useful to build scientific simulation programs?

This answer is my personal opinion. I believe that high performance numerical solvers are not a good place to use MVC pattern. Additional layers and specific data flow will not help to get a better ...