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Questions tagged [software]

Questions about libraries and standalone software designed or well-suited for scientific or numerical calculations.

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34 views

Split step Fourier method to solve Schrödinger equation for moving potential

I'm trying to use the excellent Schrodinger Python class by Jake VanderPlas (https://jakevdp.github.io/blog/2012/09/05/quantum-python/) to simulate a wave packet within a moving Gaussian potential. I ...
5
votes
1answer
128 views

Integrating/Implementing NURBS-related calculations

Recently, I started to develop some codes that use NURBS (general things I intend to use/already using: spline generation, interpolation, grids, isolines, closest-point find, and many others), both ...
0
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1answer
100 views

Which free library should I use to perform cutting/clipping operation?

I have a set of points which forms a closed loop, and I want to perform cutting/clipping a 3D model using this loop. I have used VTK but in some cases, it has a "Cannot follow edges" problem. Is ...
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0answers
29 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 ...
0
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1answer
64 views

Help understanding this numerical surface integration technique?

I'm attempting to write a FORTRAN program that calculates the magnetic field, B, at any point outside of a bar magnet. I'm going to use a first order euler scheme, where each side of the bar magnet ...
0
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1answer
194 views

Finite volume software packages

There are many software packages for the finite element method, of which the most popular are listed e.g. on Wikipedia. When it comes to the finite volume method, I'm not aware of any similarly ...
0
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1answer
44 views

Converting acceleration over time to velocity or speed in code

I have acceleration data from a sensor. X Y & Z. I move the senor in the Y axis. Mostly in a straight line. So I ignore x & z. From the sensor documentation 5.2.1 Acceleration output: ax=((...
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0answers
88 views

Solving complicated coupled ODE using RK4/ODE45 in Matlab

I have the following coupled differential equations also known as Guiding Center Approximation. It is used to explain the position- and velocity change of particles (electrons and protons, N = 1000) ...
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2answers
70 views

Software that does naïve or formal simplification of mathematical expressions

Devil-may-care that I am, suppose that I wanted to 'simplify' the following expression, utterly ignoring the fact that it's very naughty to raise various kinds of numbers to arbitrary powers or to ...
3
votes
1answer
270 views

Numerical propagation of a density matrix using Liouville von Neumann equation

I want to look at time evolution of the density matrices of some, very simple, spin systems, but I am having trouble with my approach. I want to use a simple for-...
0
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1answer
33 views

What software packages are designed towards modelling the radiation from accelerated charges?

I'm interested in modeling the electromagnetic fields radiated from an accelerated charge, but do not want to reinvent stuff if possible. I suspect there are software packages already out there which ...
0
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2answers
169 views

Is there any scalable machine learning tool like molecular dynamics software NAMD?

I work in Molecular dynamics of biomolecules. I am familiar with the software NAMD. We use NAMD in our CPU cluster with the aid of mpirun. Without GPUs can I implement large scale deep learning? ...
4
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3answers
362 views

How to solve the transcendental equation: $\tan(x) = \frac{2x}{x^2-1}$

I'm interested in finding the roots of the following equation: $\tan(x) = \frac{2x}{x^2-1}$. It is easily seen that 0 is a root and the roots are symmetric w.r.t. 0. I wonder if an analytical ...
0
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1answer
152 views

Find hidden sequence $a_n = a_{n-1} + T $ , with period $T$, given some “random” numbers

I have this data plotted on a graph in which all points have the same value on the y-axis, e.g a constant integer "c", while the x-axis is the time in seconds. So, for a c = 25 on the y-axis, there ...
0
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1answer
66 views

Most suitable particle-tracking software

I have a problem for which I am trying to determine the most suitable software to use. Here is a brief description of the problem. I have a mixture of inertial particles A and B with different ...
4
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3answers
337 views

Pre/Post-processor for an academic finite element solver

I'm currently developing a finite element solver for academic/research purposes. Therefore I'm searching for a pre- and postprocessor in my toolchain. For a previous project I have used gmsh as a ...
6
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3answers
230 views

Visualizing the solutions of the Differential equations by varying different parameters

Actually I am interested in analyzing the soution to the ODE given as $\frac{dy}{dx} = A + By + C\sin(y) , y(l) = m$ and check how the solution gets affected like whether they exist or not depending ...
0
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0answers
57 views

Software/code used to do this plot of homoclinic bifurcation

I saw this video https://www.youtube.com/watch?v=oEXeexvaAVo I find that user friendly to visualize the dynamics. I am curious on how, like on which software he did the code,also any reference guide ...
6
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2answers
182 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
0
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0answers
59 views

How to do FFT transform on unequal spaced data points? [duplicate]

How to do FFT transform on unequal spaced data points using Mathematica or Origin? My data is similar with Figure a, but the data points are unequal spaced. Does anyone know how to do FFT transform ...
2
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1answer
106 views

Extracting system matrices from FEM software

I work in the field of Finite Element Methods, specifically, developing algorithms to speed up the computational time in structural mechanics problems. Till now I have been developing my code in ...
2
votes
1answer
132 views

Any FOSS MATLAB/Octave toolbox for high-speed variable precision arithmetic?

I need to use variable precision arithmetic in MATLAB for an expensive set of computation. The vpa function provided by the symbolic math toolbox is very slow. I found a non-free alternative toolbox ...
2
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1answer
174 views

Software/code to extract a solenoidal (a.k.a. divergence-free) field from a 2D vector field numerically

Can somebody point me to software/code to extract a solenoidal (a.k.a. divergence-free) field from a 2D vector field numerically? There are a plethora of papers and documents describing how to do ...
0
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2answers
392 views

2D mesh generator with geometric primitives

The question is exactly as the title: Which 2D (triangular) mesh generator software can be used which has a set of geometric primitives, controlled mesh size and standard output (.vtk or something ...
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0answers
39 views

Software suggestion for simulating the stacking of sedimenting rods

I'd like to simulate the following problem: Define some square, horizontal and hard area onto which cylinders (aspect ratio R) sediment. Preferably, the source of cylinders sequentially generates N ...
1
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1answer
98 views

Finding the lowest $n$ eigenvalues of a band-diagonal Matrix

I have a real sparse matrix of the form $$ \left( \begin{array}{ccc} h_{11} & h_{12} & 0 & h_{14} & & & \\ h_{21} & h_{22} & h_{23} & 0 & h_{25} & & ...
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0answers
61 views

Spherical Harmonics: band-limited representations of a vector field on a sphere

I have used pyShtools in the past to expand scalar functions to spherical harmonics and to synthesize band-limited representations of them. However, I am not too sure how to achieve this for a vector ...
-4
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1answer
44 views

Why Binary language is used as a first language for the Computer Systems not a high level Language? [closed]

--> why computers not used high level language as a first Language what are the main reasons?
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0answers
41 views

Book Recommondation for the time-dependent Schrödinger equation [duplicate]

Can you recommend a good book that discusses several methods for the numerical solution of time-dependent and time-independent Schrödinger equation? I have searched the internet several times but ...
7
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0answers
124 views

What is some of the best software design you've seen in a numerical code? [closed]

I don't think I've ever seen any scientific computational software that I would consider "good" in terms of software design. I don't mean in terms of functionality, but in terms of good high-level ...
1
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2answers
57 views

Automatic motion recognition

How difficult is it to program an automatic software using C that is able to read astronomy images of up to 4096x4096 pixels (or other sensor geometries), search ...
0
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2answers
89 views

Integrating a dynamical system until an algebraic condition is satisfied

I have a model given by a system of differential equations $$ \frac{dy}{dt}=f(y)$$ with $y=(y_1,y_2,y_3)$ and $f:\mathbb{R}^3 \to \mathbb{R}^3$. The system works as follows : integrate the ode's ...
1
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0answers
127 views

What are alternatives to openbabel to convert CML file to image?

I recently started to perform natural resonance theory (NRT) analysis with NBO6. This program may automatically create a chemical markup language (cml) file with the treated structures. Unfortunately ...
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0answers
63 views

Convolutional Neural Nets for Large Scale Image Classification on Windows?

I need to build some CNN's using very large numbers of photos, to classify which photos contain certain features. I've run into a number of road blocks. As much as I love both Linux and ...
1
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1answer
112 views

Is OPENFOAM a good idea for direction/operator splitting in parabolic equation

I would like to know if I should switch to OPENFOAM for my task. I work only with Cartesian grids, right now in 2d, rectangular domains only. If $\mathbf{w} = (w_1, w_2)$ and suppose I want to solve ...
3
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0answers
45 views

Numerical Euler Rotation Equation

The problem I have may be really simple, but still getting a hard time solving it. So I have the Euler rotation equations: $$I_{1}\dot{\omega}_{1}+\left(I_{3}-I_{2}\right)\omega_{2}\omega_{3}=\...
3
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0answers
135 views

Evaluation of feynman diagrams: FORM vs. Sympy vs. other

I just started working on my master thesis in the theoretical particle physics and my supervisor asked me to start working with FORM, a script interpreter with basic knowledge of lorentz and dirac ...
7
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1answer
208 views

Does some form of documentation of GMSH exist?

I am looking to implement GMSh into a simualtor that I am going to create. I am looking to integrate the geo, mesh, and post processor modules. However, looking online, it appears the documentation ...
1
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0answers
90 views

Which topics are hot in computational science? [closed]

I am accepted to computational science master program. The master program just started to accept students in our university and today each group of 3 students was assigned to an advisor teacher (we ...
1
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0answers
35 views

Interior nodes of a closed graph?

Does anybody know if any graph partitioner library such as Metis, Scotch, or Zoltan can (besides splitting a domain), differentiate between internal (i) and boundary (b) nodes?
1
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0answers
42 views

Manipulating/Extracting Data and Developing Methods - Language Choice [closed]

As a general programming enthusiast and aspiring Bioinformatician student I have an intermediate understanding of computing (languages) as well as Java, and to a lesser extent C++. Having knowledge in ...
4
votes
2answers
116 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 ...
6
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3answers
414 views

Fluid-structure interaction solver for cardiovascular applications

I would like to start running FSI simulations for cardiovascular applications. More precisely, I'm interested in the behaviour of aortic valve under physiological flow conditions in which the ...
7
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1answer
409 views

Python trust region optimization code that allows ellipsoid-shaped trust regions

Are there any high quality trust region optimization implementations that allow nonspherical ellipsoid trust regions, and are written in Python, or are easy to call from python? By nonspherical ...
0
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1answer
78 views

Mechanics - Rotational Inertia

I am facing a problem solving a mechanical system which is shown in the scheme below. We assume that coupling of the two shafts is done with a clutch Equations: $$J1*\frac{d\omega1}{dt} + Td(\...
11
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2answers
554 views

Danger of complex arithmetics in scientific computing

The complex inner product $\langle u,v\rangle$ has two different definitions decided by conventions: $\bar{u}^Tv$ or $u^T\bar{v}$. In BLAS, I found the routines cdotu, zdotu, and cdotc, zdotc. The ...
0
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1answer
69 views

What are some tips on developing a problem-specific ODE solver?

I have a small system of stiff ODEs describing a chemical reaction. The right-hand side is quite complicated, as well as the Jacobian. This equation will be solved many times with different initial ...
0
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1answer
203 views

Mac/Xcode/C++ connect with GAMS

Basically, I failed to trying to implement individual global MINLP solvers (alphaBB, ANTIGONE, BARON, Couenne, LindoAPI, and SCIP) in C++/Xcode/Mac system. On the other hand, I realize that GAMS ...
1
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2answers
69 views

Help on writing sofware: general guidelines, in particular separation of computation and visualization

Although I already did some work in the intersection of theory and simulation I'm still very new to this field and I need some guidance. If anybody can give some recommendations for introductory ...
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3answers
311 views

C++ mixed integer nonlinear programming (MINLP) solver

Doing research project in material involving (mixed integer nonlinear programming) MINLP problem, we want to implement MINLP based on C++, because the majority of our project is based on C++. What ...