Questions tagged [software]

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

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Software for Feasibility Problems

I face a feasibility problem of type $$ c_i(\boldsymbol x) \leq 0, i = 1, \dots, \mathcal{I} \\ c_e(\boldsymbol x) = 0, e = 1, \dots, \mathcal{E} $$ where $\mathcal{I} + \mathcal{E} \gg \text{dim}(\...
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Book recommendation request: A good C++ based software development book for a computational mathematician

I'm hoping that this type of question is on-topic, and I have put in a little hunting to make sure it isn't a flat out repeat. If it is either of the above, I apologize in advance. I'm an early career ...
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How can I couple MCNP with FLUKA? To attain reactor dynamics and simulate an ADS experiment? (Under Subcritical fast system)

I'm new in Particle Physics based Computing. I want to simulate an ADS experiment (Accelerator Driven System) in subcritical fast system. I was advised to simulate the experiment with FLUKA with MCNP ...
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3 answers
85 views

How can I plot a rainbow?

I'm trying to write a program that can simulate a rainbow. So far I've got figured out how to determine the change in the refractive index depending on the wavelength, the angular deviation of the ...
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Convoluted exponential gaussian probability function from Igor Pro

I am trying to figure out the exact formula for a three convoluted exponential gaussian probability function from the software Igor Pro, from my research. Unfortunately all I the closest equation from ...
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How to solve nonlinear second order ODE in Matlab? [duplicate]

I am working on simulating a car suspension system using Matlab. Specifically, I have to derive equation of motion using the Lagrange method and then use ode 45 to solve it. However, while using ...
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2 votes
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Continuum solutions for the Dirac equation in Coulomb potential - numerical codes

Following the representation used in [1, pag. 11] the solution of the Dirac equation in polar coordinates for energy $E$ is of the type: $$ \psi_{E\kappa m}(\bf{r})= \dfrac{1}{r} \Bigg( \begin{matrix} ...
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2 votes
1 answer
408 views

Reference request: C++ and numerical analysis book

I'm a master student with a good Numerical analysis background. I'm going to do a master thesis in the same subject, but I need to use C++ since my advisor loves it, and I also believe it's the best ...
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1 vote
2 answers
328 views

Diagonalization using LAPACK

Say, we have a Hamiltonian which for simplicity does not mix particle hole sectors. It is just a simple Hamiltonian in real space as shown, $H=\sum_{ij,\sigma} A(i,j)(c_{i\sigma}^{\dagger}c_{j\sigma} +...
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174 views

Numerical minimization of the action in python

I want to find the trajectory $x(t)$ which minimizes the action $S = \int_{t_i}^{t_f} L(x(t), \dot{x}(t)) \mathrm{d}t$ numerically. I am trying to do it by discretizing the action so it is more of a ...
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3 answers
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Draw magnetic field lines or vector field of a magnetic dipole - Python/Matplotlib

In the Wikipedia article on magnetic moments, subsection "Effects on environment" defines the magnetic field H of a magnetic dipole moment. Additionally the magnetic field lines of this ...
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347 views

Open-source Hexahedral meshing tools

I'm looking for an open-source automatic meshing tool or library able to generate full or dominant hexahedral mesh starting from a provided arbitrary model i.e. a surface triangular mesh stored in STL ...
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Trouble Estimating Motor Parameters with Least Squares in MATLAB

Basically, I'm trying to use Least-Squares to estimate the parameters of a DC motor. My system can be modeled by the following matrix equation: $$\begin{bmatrix}V_{input}(t)\\0\end{bmatrix}=\begin{...
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1 answer
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Solution of Coupled Differential equation for a 2d linear flow using RK4 method in python 3

I want to study the dynamics of a 2d linear flow, whose dynamical equation is- $\begin{pmatrix} \dot{x_1}\\ \dot{x_2}\\ \end{pmatrix}=\begin{pmatrix} 1 & 1\\ 4 & -2\\ \end{pmatrix}\begin{...
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8 votes
2 answers
14k views

How to properly calculate CPU and GPU FLOPS performance?

Problem I'm trying to calculate CPU / GPU FLOPS performance but I'm not sure if I'm doing it correctly. Let's say we have: A Kaby Lake CPU (clock: 2.8 GHz, cores: 4, threads: 8) A Pascal GPU (clock: ...
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1 vote
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I'm trying to add a colour to the LogicalVolume in Geant4. I get the error that fVisAttributes and visAttributes are undefined. How can I fix this?

I'm trying to add a colour to the LogicalVolume which has been renamed to TrackerLogical in Geant4. I get the error that fVisAttributes and visAttributes are undefined although I have defined them in ...
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6 votes
3 answers
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Coroutines for ODE solvers

Are there any ODE solver packages that use coroutines and yield their results instead of functions and returning? Briefly, a subroutine in a programming language does some computations, returns a ...
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2 votes
2 answers
217 views

Writing code on the CPU while developing, running it on the GPU when live - which approach?

In my simulations I am using dense matrix-vector multiplications and 2D-fft transformations quite often, for matrix sizes of 8kx8k and up. Hence, I assume that using a GPU is beneficial for speeding ...
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Is it possble to do this complex symbolic calculation with Matlab?

Sorry it's bit abrupt, but recently I am caught up in some symbolic calcualtion which is tedious and almost impossible with mere human hands, so just wondering is it possible to solve the double ...
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15 votes
3 answers
622 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 ...
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1 vote
1 answer
94 views

Manual for library Libxc

Where can I find the manual for software library Libxc for exchange-correlation functionals? Links with domain www.tddft.org don't work.
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1 answer
442 views

How should errors be reported in scientific libraries?

There are many philosophies in different software engineering disciplines about how libraries should cope with errors or other exceptional conditions. A few of the ones I've seen: Return an error ...
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1 vote
1 answer
77 views

Best way of storing numerical data in a compact manner, while leaving it accessible for tools like GnuPlot?

My simulation, written in C++, generates a large amount (roughly ~500) of text files for each set of parameters I try to simulate, with four columns of ~5k double values in each file. Furthermore, to ...
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1 vote
1 answer
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Software for parallel incomplete LU factorisation

I am looking for a software package to compute incomplete LU factorisations in parallel. Further considerations are: The package must allow for arbitrary level-of-fill or threshold-based truncation. ...
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1 vote
3 answers
64 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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4 votes
3 answers
932 views

Best software to do big number calculations quickly

I am trying to do some work on some math conjecture. I am testing the conjecture numbers using very large math numbers (100+ digits ). I am currently using python to test these numbers. In the ...
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5 votes
1 answer
321 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 ...
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1 answer
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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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1 vote
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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 ...
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0 votes
1 answer
97 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 ...
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1 answer
866 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 ...
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1 answer
121 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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1 vote
0 answers
244 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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2 answers
80 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 ...
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4 votes
1 answer
897 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-...
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0 votes
1 answer
40 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 ...
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0 votes
2 answers
256 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? ...
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4 votes
3 answers
3k 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 ...
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1 answer
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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 ...
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1 answer
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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 ...
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4 votes
3 answers
1k 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 ...
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5 votes
3 answers
562 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 ...
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5 votes
2 answers
670 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
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3 votes
1 answer
152 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 ...
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1 vote
1 answer
371 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 ...
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3 votes
1 answer
286 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 ...
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0 votes
2 answers
893 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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1 vote
0 answers
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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 ...
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1 vote
1 answer
167 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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1 vote
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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 ...
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