Questions tagged [software]
Questions about libraries and standalone software designed or well-suited for scientific or numerical calculations.
187
questions
2
votes
1
answer
77
views
Good IDE for GNU Octave?
Are there any good IDEs for working with Octave code?
I'm used to type hints and documentation preview from software like IntelliJ or VS Code. While there are syntax highlighting plugins for VSC, all ...
- 121
1
vote
1
answer
98
views
Issue in implementing a cloth simulation using verlet integration
I am trying to implement a cloth simulation in c++ using verlet integration and I'm getting some odd issues that I can't seem to explain, the points in the cloth seem to fly around and have weird ...
- 31
0
votes
0
answers
29
views
Geant4, simulate photon emitted into lead
I have just learned Geant4 and recently I tried to simulate photons emitted into lead. After I collected the data and figured out the transmission of photons. I found my data is bigger than the ...
- 9
7
votes
4
answers
1k
views
Euler integration of the three-body problem
Me and one of my colleague are trying to simulate the three-body problem with a C++ program in order to compare different integration schemes. At the moment we are trying to use the Euler's method, ...
- 171
1
vote
0
answers
52
views
Implementations of the Eisenstat-trick for SSOR
Where can I find a source code for the SSOR method with Eisenstat's trick?
The original paper includes pseudo code but also seems to have minor typos. For that reason, I would be very happy to see an ...
- 3,570
2
votes
0
answers
41
views
Software for Smith form or Hermite form of a sparse polynomial matrix
In a current research project, I have a number of matrices with coefficients in ℚ[𝑥] for which I want to understand how their rank depends on the value of the parameter 𝑥.
These matrices are:
...
1
vote
0
answers
51
views
I need MATLAB or Mathematica code to solve this integral over limit 0- λ
I want the code to integrate equation(1) or (2) over the limits using mathematical or mathlab to get equation (3) as the answer of $Z$ vibrational partition function, giving the following additional ...
5
votes
1
answer
90
views
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}(\...
- 809
0
votes
0
answers
80
views
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 ...
- 113
0
votes
0
answers
34
views
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 ...
- 11
0
votes
3
answers
87
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 ...
- 1
0
votes
1
answer
72
views
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 ...
- 11
0
votes
0
answers
42
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 ...
Luận Trần Công
2
votes
0
answers
65
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:
$$ \psi_{E\kappa m}(\bf{r})= \dfrac{1}{r} \Bigg( \begin{matrix}
...
- 21
2
votes
1
answer
495
views
Reference request: C++ and numerical analysis book
I'm a master student with a good Numerical analysis background. I'm going to do a master thesis in the same subject, but I need to use C++ since my advisor loves it, and I also believe it's the best ...
- 211
1
vote
2
answers
538
views
Diagonalization using LAPACK
Say, we have a Hamiltonian which for simplicity does not mix particle hole sectors. It is just a simple Hamiltonian in real space as shown,
$H=\sum_{ij,\sigma} A(i,j)(c_{i\sigma}^{\dagger}c_{j\sigma} +...
- 13
1
vote
2
answers
219
views
Numerical minimization of the action in python
I want to find the trajectory $x(t)$ which minimizes the action $S = \int_{t_i}^{t_f} L(x(t), \dot{x}(t)) \mathrm{d}t$ numerically.
I am trying to do it by discretizing the action so it is more of a ...
murt_
0
votes
3
answers
3k
views
Draw magnetic field lines or vector field of a magnetic dipole - Python/Matplotlib
In the Wikipedia article on magnetic moments, subsection "Effects on environment" defines the magnetic field H of a magnetic dipole moment. Additionally the magnetic field lines of this ...
- 35
1
vote
0
answers
598
views
Open-source Hexahedral meshing tools
I'm looking for an open-source automatic meshing tool or library able to generate full or dominant hexahedral mesh starting from a provided arbitrary model i.e. a surface triangular mesh stored in STL ...
- 11
-1
votes
1
answer
46
views
Trouble Estimating Motor Parameters with Least Squares in MATLAB
Basically, I'm trying to use Least-Squares to estimate the parameters of a DC motor.
My system can be modeled by the following matrix equation:
$$\begin{bmatrix}V_{input}(t)\\0\end{bmatrix}=\begin{...
- 109
1
vote
1
answer
397
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{...
11
votes
3
answers
21k
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: ...
- 211
1
vote
0
answers
76
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 ...
- 11
6
votes
3
answers
159
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 ...
- 9,003
2
votes
2
answers
251
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 ...
- 543
0
votes
0
answers
57
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 ...
- 1
15
votes
3
answers
691
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 ...
- 353
1
vote
1
answer
100
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.
- 331
11
votes
1
answer
444
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 ...
- 9,003
1
vote
1
answer
89
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 ...
- 543
1
vote
1
answer
168
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. ...
- 425
1
vote
3
answers
75
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?
4
votes
3
answers
1k
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 ...
- 143
5
votes
1
answer
333
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 ...
- 8,552
0
votes
1
answer
115
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 ...
- 1
1
vote
0
answers
65
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
votes
1
answer
110
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 ...
- 3
0
votes
1
answer
966
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 ...
- 442
0
votes
1
answer
136
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=((...
- 101
1
vote
0
answers
249
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) ...
J.Doe
0
votes
2
answers
81
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 ...
- 195
4
votes
1
answer
987
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
votes
1
answer
43
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 ...
- 101
0
votes
2
answers
275
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?
...
- 81
4
votes
3
answers
4k
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 ...
- 143
0
votes
1
answer
158
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 ...
- 101
0
votes
1
answer
111
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 ...
- 23
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 ...
- 186
5
votes
3
answers
591
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 ...
- 229
5
votes
2
answers
801
views
Speeding up a linear transform using Python
In an optical wavefront propagation problem, I need to do excessive Fourier-type computations:
...
- 151