Questions tagged [python]

A general purpose high-level programming language that emphasizes ease of code syntax and readability.

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12
votes
2answers
6k views

Solving a least squares problem with linear constraints in Python

I need to solve \begin{alignat}{1} & \min_{x}\|Ax - b\|^2_{2}, \\ \mathrm{s.t.} & \quad\sum_{i}x_{i} = 1, \\ & \quad x_{i} \geq 0, \quad \forall{i}. \end{alignat} I think it is a ...
8
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2answers
3k views

Updatable SVD implementation in Python, C, or Fortran?

I would like to do evolving factor analysis using the SVD: Given $m \times n$ data matrix $\mathcal{A}$, and for each $i$ from 1 to $m$, I want to calculate the singular values of: $$\mathcal{A}\...
7
votes
5answers
9k views

Interpolate 2D data

I generated a cartesian grid in Python using NumPy's linspace and meshgrid, and I obtained some data over this 2D grid from an ...
7
votes
3answers
857 views

How to handle large numbers of output data sets from a simulation/sensitivity analysis?

Somewhat related, but I think the question is distinct enough to justify a separate question. As a bit of background, I come from a observational/statistical Epidemiology background, working with ...
30
votes
4answers
2k views

What tools or approaches are available to speed up code written in Python?

Background: I think I might want to port some code that calculates matrix exponential-vector products using a Krylov subspace method from MATLAB to Python. (Specifically, Jitse Niesen's expmvp ...
19
votes
5answers
3k views

Parallel Scientific Computation Software Development Language?

I want to develop a parallel scientific computation software from scratch. I want some thoughts on which language to start. The program involves reading/writing data to txt files and doing heavy ...
11
votes
1answer
5k views

Algorithms for community detection for bipartite graphs?

Are there any algorithms for community detection for bipartite graphs (2-mode networks) implemented in igraph, networkX, R or Python etc.? In particular, is there such an implementation in which one ...
0
votes
1answer
2k views

1d shock tube problem, and the solution [closed]

I have solved 1d shock tube problem. (Euler's equations). Using following steps: 1) Define Riemann problem over the domain 2) Carry out local linearisation 3) Based on linearisation, write eigen ...
16
votes
2answers
2k views

(how to) write simulations that run faster?

I have started using python as the programming language for doing all my assignments in CFD. I have a very little experience in programming. I am from mechanical engineering background and am pursuing ...
8
votes
2answers
7k views

Solving non-linear singular ODE with SciPy odeint / ODEPACK

I want to solve the Lane-Emden isothermal equation [PDF, eq. 15.2.9] $$\frac{d^2 \!\psi}{d \xi^2} + \frac{2}{\xi} \frac{d \psi}{d \xi} = e^{-\psi}$$ with the initial conditions $$\psi(\xi = 0) = 0 \...
28
votes
8answers
6k views

Which package should I use to wrap Modern Fortran Code with Python?

I know of, and have used f2py2e to wrap some old Fortran 77 code, but my understanding is that it does not work with newer Fortran 95 code. I've researched what I should use, and have come across ...
25
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3answers
16k views

Recommendation for Finite Difference Method in Scientific Python

For a project I am working on (in hyperbolic PDEs) I would like to get some rough handle on the behavior by looking at some numerics. I am, however, not a very good programmer. Can you recommend ...
29
votes
9answers
2k views

What is a good way to run parameter studies in C++

The problem I'm currently working on a Finite Element Navier Stokes simulation and I would like to investigate the effects of a variety of parameters. Some parameters are specified in an input file ...
11
votes
2answers
2k views

Efficiency of using petsc4py vs. c/c++/fortran

How much slower is petsc4py vs c/c++/fortran? I realize it will depend significantly on the code being executed, but what about something simple like a matrix-vector product?
12
votes
4answers
1k views

Making a Molecular editor/visualizer: Object oriented programming, data structures, and molecules

I am new to programming and I am trying to solve my first big problem and write my first big program. I have looked for open source examples of code to learn from, but so far have only found code in ...
8
votes
1answer
19k views

scipy.optimize.fmin_bfgs: "Desired error not necessarily achieved due to precision loss"

I am getting the warning in the post subject when attempting to optimize a function in Python with the scipy.optimize.fmin_bfgs function. The complete output: Warning: Desired error not necessarily ...
12
votes
4answers
5k views

What are the best Python packages/interfaces to sparse direct solvers?

Please list the Python package (petsc4py, etc...) and the sparse direct solvers it supports. One (community-wiki) answer per package, please.
3
votes
0answers
160 views

Is there an easy way to read a PetscBag into a python dict?

I'm using a PetscBag to store the input parameters of my program. At some point, I'm going to need to use python to plot these parameters against some output parameters, and ...
15
votes
3answers
2k views

I/O Strategies for computational problems with large data sets?

My research group focuses on molecular dynamics, which obviously can generate gigabytes of data as part of a single trajectory which must then be analyzed. Several of the problems we're concerned ...
3
votes
0answers
70 views

Understanding how Numpy does SVD [duplicate]

Possible Duplicate: Understanding how Numpy does SVD I have been using different methods to calculate both the rank of a matrix and the solution of a matrix system of equations. I came across the ...
13
votes
3answers
8k views

Understanding how Numpy does SVD

I have been using different methods to calculate both the rank of a matrix and the solution of a matrix system of equations. I came across the function linalg.svd. Comparing this to my own effort of ...
5
votes
1answer
1k views

Drawing isocontour data of 3d discrete volume with mayavi2

I'm trying to visualize the propagation of heat in a discrete sphere surface. The sphere is hollow, only the voxels of the boundary have value. Visualization in matlab using isosurface shows correct ...
11
votes
4answers
7k views

solving coupled ODEs with initial-value and final-value constraints

The essence of my question is the following: I have a system of two ODEs. One has an initial-value constraint and the other has a final-value constraint. This can be thought of as a single system with ...
29
votes
2answers
28k views

Define custom probability density function in Python

Is there a way, using some established Python package (e.g. SciPy) to define my own probability density function (without any prior data, just $f(x) = a x + b$), so I can then make calculations with ...
31
votes
8answers
2k views

Scientific workflow management system

Can anyone recommend me a good workflow management system (WMS), preferably in Python? So far I have been using GNU Make, but it introduces a layer of complexity that I want to avoid. A good WMS ...
3
votes
1answer
1k views

Solve log equations problem [SageMath]

Input var('x') solve((log((x**2 - x), 6) - log((6*x - 10), 6) == 0), x) Output [log(x^2 - x) == log(6*x - 10)] But real ...
8
votes
4answers
4k views

High Order derivatives of splines using SciPy

I have created a spline to fit my data in python using: spline=scipy.interpolate.UnivariateSpline(energy, fpp, k=4) The equation I want to use involves a ...
5
votes
6answers
19k views

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 &...
11
votes
4answers
605 views

Runge-Kutta and Reusing Datapoints

I am trying to implement the fourth order Runge-Kutta method for solving a first order ODE in Python i.e. $\frac{dy}{dx} = f(x,y)$. I understand how the method works, but am trying to write an ...
8
votes
2answers
446 views

Filtering a dataset to get a more uniform distribution for neural network training

I'm looking into using artificial neural networks (ANN) to predict the reaction rates in my fluid instead of solving the full system of stiff ODEs. Some people from my lab have already done some work ...
1
vote
0answers
81 views

Constraint solving over modular domains

I have a set of constraints over modular domains e.g. $\exists a \in A_i : x \equiv a \pmod{n_i}$ for all $i=0,\ldots,k$ The question is, does such an $x$ exist? I've been pointed to method of ...
5
votes
1answer
2k views

creating a flat surface in python

I'm trying to create a figure of particle distribution from a reference surface in python. I plan to get a distribution in python and then prettify it with tikz. I tried this: ...
7
votes
6answers
8k views

Python implementations of Gillespie's direct method

I'm looking for a decent implementation of Gillespie's Direct Method in Python, as if I code the algorithm myself I'm nigh positive I'll do it inefficiently. Anyone have a favorite?
88
votes
18answers
111k views

Is there a high quality nonlinear programming solver for Python?

I have several challenging non-convex global optimization problems to solve. Currently I use MATLAB's Optimization Toolbox (specifically, fmincon() with algorithm=<...

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