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

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21 views

GNU Software to construct crystal superlattices

I am looking for software recommendations. I want to know if there is any GNU visualization software that is capable of of joining two periodic crystals. For example, I want to be able to join a slab ...
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2answers
64 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 ...
0
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0answers
9 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
20 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 ...
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0answers
41 views

Rotation of acceleration data into earth frame using quaternions [closed]

I am working on a project to find displacement using accelerometer and gyroscope. The problem I am facing is, when I rotate the acceleration data measured in body frame to the earth or initial frame ...
1
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1answer
51 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
40 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: ...
3
votes
0answers
45 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 ...
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0answers
104 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
75 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 ...
0
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0answers
19 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?
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0answers
43 views

Available Software packages for setting initial configuration

I have just started learning Molecular Dynamics using dl_poly_classic and analysing trajectory using nMOLDYN. For this purpose, I want to construct a micellar system of (say of single micelle) in my ...
1
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0answers
39 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
109 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 ...
3
votes
2answers
116 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 ...
5
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0answers
136 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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0answers
170 views

Numerical solution to 1D Schrödinger equation

I was trying to solve 1D Schrödinger numerically for a few example potentials, using the most minimalistic approach possible. There is a problem that baffles me, but I can't figure out what's causing ...
0
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1answer
75 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} + ...
11
votes
1answer
460 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
votes
1answer
57 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
votes
1answer
100 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
vote
2answers
62 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 ...
0
votes
2answers
125 views

c++ minlp solver

Doing research project in material involving (mixed integer nonlinear programming) MINLP problem, we want to implement MINLP based on c++, because majority of our project is based on c++. What would ...
2
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1answer
125 views

non-smooth convex c++ solver

I happened to know that there are advanced established techniques for non-smooth convex optimization in research. For example, these two papers: Nesterov, "Smooth minimization of non-smooth ...
0
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0answers
50 views

Is there an existing library that calculates all modes in a step index fiber?

Before embarking on this task I thought it wise to ask if anyone knows of an existing library that does this. I would be coding it in python and at least for starters work on the assumption that ...
5
votes
1answer
100 views

Additional cost associated with quad (or higher) precision

In going from double precision to quad (or higher) precision, roughly how much of a performance hit is taken on various architectures and frameworks. Do floating point operations take twice as much ...
1
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2answers
108 views

convex optimization with objective function given by oracles

Is there any solver for convex optimization in C++ (or some dedicated scheme while no solver is yet available) that could solve a convex optimization problem with objective function value given by an ...
0
votes
1answer
74 views

MAX-SAT pseudo-boolean optimization(PBO) weighted boolean optimization(WBO) solver

I have come across (state of the art) softwares on MAX-SAT PBO or WBO: examples are WBO, open-WBO, SAT4J, scip. They all seem to work in a way that only command line instruction is involved. I want to ...
3
votes
2answers
2k views

Programming Finite Element Methods in C++

I am trying to develop a library for finite element methods in C++ and for that I am looking at the data structures for meshes. Based on what I've read up on fenics and deal.ii, the general ...
2
votes
1answer
122 views

Poisson solver diverged

My 2D-Poisson solver is build for simulation of semiconductor. The algorithm is Gauss-Seidel iterative method. If I use simple PN junction for simulation testing, it diverged while I applied high ...
0
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0answers
50 views

Results from TLE & SGP4 propagation - don't seem right & need help with interpretation [closed]

I acquired a TLE of the ISS from internet and used the C++ SGP4 propagator to compute future position and velocity vectors of the Station. I am a little unsure about some aspects of results though and ...
1
vote
4answers
252 views

Soft question: What are good libraries for solving ordinary differential equations?

I am aware of a few: a) R project b) Intel® Ordinary Differential Equations Solver Library But, I'd like to know which are the best tools that have been developed by professional physicists and ...
2
votes
2answers
589 views

Using Trilinos and/or Petsc in Windows with Visual Studio?

I am currently working on a project of building a simulator. Up till now I have mostly played around with very simple examples, but with regards to the future I have been thinking that it might be a ...
1
vote
1answer
249 views

Solving a problem using multiple threads using CLP

Is it possible to run Clp on multiple threads using Julia and JuMP?
1
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0answers
30 views

Understanding the use of Minimum Translation Vector (MTV) for an elastic collision response

So, I'm trying to simulate polygon rigid body physics, both linear and angular. To calculate the MTV is easy in SAT (Minimum Translation Vector), and to use it to adjust position is also easy: ...
7
votes
1answer
102 views

Do C++ matrix libraries translate compound vector operations to single loops?

I am trying to replicate Fortran90 array syntax using a C++ library. The libraries themselves are discussed at length in this question. They can all do something like this: ...
7
votes
4answers
271 views

Should I use a database to handle large amounts of results?

Background: I am currently running a large amount parameter variation experiments. They are being run in Python 2.6+, using numpy. These experiments are going to take about 2 weeks to run. Roughly I ...
5
votes
3answers
397 views

FOSS tools for creating high quality physics animations and simulations in 2d and 3d

If I want to create a high quality figure to illustrate a scientific concept or experiment I usually use tikz together with ...
3
votes
2answers
87 views

Automated software optimization and tuning

I'm writing code that uses a lot of graph operations; many higher-level algorithms iterate over all the graph edges and do some processing on them. There's an iterator method that returns a batch of ...
3
votes
2answers
412 views

Tool for computing electric field on a 3d surface

I'm looking for software recommendations for an electrostatic simulation: I have a 3d object of uniform, high conductivity, separated from its environment by a high-resistance skin. Inside that ...
0
votes
0answers
86 views

Recursive code that uses Newton's method to calculate bands of the Kronig Penney model [closed]

Can someone help or give me some input writing a program (matlab) preferable, that will recursively calculate the bands of the Kronig Penney model? Unfortunately, I haven't taken any computer class ...
1
vote
0answers
266 views

An efficient way to convert between MKL and Armadillo types

We use Armadillo a lot in our code but there are places where we prefer to use MKL directly from Vector Math Library. We have cx_vec i.e. vector of doubles. But the exp function of armadillo uses ...
0
votes
0answers
567 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 ...
3
votes
1answer
273 views

Sparse quadratic programming solver

For a hobby project I need to solve a series of quadratic programming problems each with about 500 variables about 1000 constraints, each of the form $x_i-x_j\le c_{ij}$ the objective function is ...
0
votes
1answer
60 views

Angular Velocity by Vector - 2D [duplicate]

This is originally a problem in programming, but since almost no one on Stackoverflow know how to solve this I went here instead; ...
0
votes
1answer
64 views

Getting wrong results when calculating Physics [closed]

Im making a physics app where im calculating a projectile and im using forces to calculate the acceleration but im getting some pretty strange results when calculation the drag and magnus effect. I ...
2
votes
1answer
502 views

Celestial mechanics simulation software? The 'N-Body Problem'

What software or sites might simulate an N-body gravitational problem? Application is related to Klemperer Rosette or Iridium Satellites. Bias for C, C++, PHP, or Java. Nice visuals a big plus. ...
4
votes
1answer
247 views

User Friendly GUI based 3d PDE solving software

I'm searching for software which can solve 3d IBVP like PDEtool in Matlab (user-friendly GUI, easy to learn how to use). What could you advise to me? (ANSYS,COMSOL,OpenFOAM are too difficult for me)
0
votes
1answer
46 views

Best way of getting updates on intermediate simulation results

I will be interfacing our fluid dynamics code with an optimizer. I expect the optimization process to take 3-4 days for any decent decrease. But I will want to have a look at the intermediate results ...
0
votes
1answer
172 views

What libraries provide an implementation of multigrid?

I am working on numerical method of Multigrid. What's the available implementation(solver) (actually used in scientific computation) of multigrid method?