Questions tagged [software]

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

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11 views

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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49 views

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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1answer
251 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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2answers
142 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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2answers
86 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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3answers
525 views

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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3answers
535 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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2answers
6k 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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24 views

How to define "Characteristic length in Ansys CFX Power Syntax script?

I am trying to evaluate Reynolds number in Ansys CFX 2020 R2 using CCL/Perl script on different domains in a radial turbine. But for that, I need to define the Characteristic length. So I define the ...
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107 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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1answer
38 views

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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1answer
95 views

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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6answers
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How can I plot piece-wise defined function in some easily-accessed open-source tool?

I want to plot $$f_{n}(x) = \begin{cases} x-n & \text{for } n \leq x \leq n+1 \\ 2-x+n & \text{for } n+1\leq x \leq n+2 \\ 0 &...
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0answers
32 views

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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2answers
135 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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3answers
136 views

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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54 views

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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11answers
2k views

Venues for publishing papers that emphasize software

Software is a fundamental part of computational science, and is increasingly recognized as an essential part of the scientific record. Given the value of using existing and well-tested code, it seems ...
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1answer
91 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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1answer
429 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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8answers
4k views

What software is good to use for parallel debugging?

I'm not running any parallel code right now, but I anticipate running parallel code in the future using a hybrid of OpenMP and MPI. Debuggers have been invaluable tools for me when running serial ...
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1answer
69 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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3answers
953 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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1answer
104 views

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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1answer
66 views

Efficient calculation for L-Kurtosis?

I am doing some statistical signal analysis and was wondering if there are any C/Java packages that do L-moment calculations, specifically L-Kurtosis as I am wanting to do things such as ...
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2answers
4k views

Open-source 3D FEM Solver for Electromagnetics (Time-Harmonic Maxwell)

I was wondering if there exist any good (accurate/fast/easy-to-use) open-source FEM solvers for 3D time-harmonic Maxwell's equations. I am looking to simulate systems a few wavelengths large in the X/...
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2answers
203 views

Using computational libraries on a machine without root access

If you want to use a computational library on a high-performance computing center where you have no root access to install new software you can use header-only template libraries such as MTL4, Eigen3, ...
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3answers
127k views

What is the simplest way to do a user-local install of a python package?

I don't want to deal with virtualenv for a local Python installation, I just want to install a few packages locally without dealing with the PYTHONPATH environment ...
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1answer
2k views

Free HFSS alternative to create geometry using python

I am using a python script to create wirebond interfaces in Ansys HFSS. Variables define the board, wirebond, and package geometry. To simulate a new wirebond, I just edit the geometry variables and ...
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8answers
2k views

What are good ways to document scientific software?

Many times, when I've inherited or encountered scientific code written by other people (or occasionally, even my own work), I've noticed that documentation is either sparse or nonexistent. If I'm ...
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3answers
650 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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4answers
412 views

What would be the most helpful way to write code for a paper so that readers can clearly match the results to the code that generates them?

I'm writing a reproducible paper, and the paper has computational results that are generated by a Python script (a similar MATLAB script generates nearly identical results). I feel that the paper ...
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1answer
564 views

Can TETGEN generate triangulation of a 2D point set?

I would like to link my Fortran 90 application to a library which would give me Delaunay triangulation (for a 2D set of points) and tetrahedralization (for a 3D set of points). As suggested in Fastest ...
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8answers
131k views

Recommendations for a usable, fast C++ matrix library?

Does anyone have recommendations on a usable, fast C++ matrix library? What I mean by usable is the following: Matrix objects have an intuitive interface (ex.: I can use rows and columns while ...
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1answer
34 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
2k views

PDE discretization with the method of rothe and the method of lines (Modular implementation)

The Heat equation is discretized in space with FV (or FEM), and a semi-discrete equation is obtained (system of ODEs). This approach, known as the method of lines, allows to easily switch from one ...
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1answer
112 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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5answers
269 views

Computational science contests. Why arent there any?

I was wondering why there are no online or offline computational science contests? At least I couldn't find much by googling. I mean, like a topcoder for computational sciences. I assume one reason is ...
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2answers
246 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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2answers
130 views

C++ library to mutate pdb residues

Are there any open source libraries available to mutate PDB protein residues? If so are do you have any examples of them?
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1answer
294 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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1answer
156 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 ...
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3answers
1k 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 ...
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1answer
145 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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1answer
308 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 ...
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0answers
58 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 ...
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1answer
89 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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1answer
84 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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1answer
664 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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3answers
795 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 ...