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Questions tagged [data-structures]

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1
vote
1answer
86 views

How to generate a face list from vertices?

I have a little background in writing toy finite volume CFD codes. In 2D Cartesian scenarios, I typically take $x_{\min}$, $x_{\max}$, $y_{\min}$, $y_{\max}$, and the number of points in $x$ and $y$ ...
9
votes
1answer
126 views

bit-packing and compression of data structures in scientific computing

I recently came across this paper, which describes a scheme for saving memory in representing sparse matrices. A 32-bit integer can store numbers up to ~4 billion. But when you solve a PDE you've gone ...
2
votes
1answer
86 views

Union of closed intervals on $\mathbb{R}$

Suppose there are multiple intervals on $\mathbb{R}$, e.g., $[0,0.5]$, $[0.4,1]$, $[1.5,2]$, the union of them should be $[0,1]$ and $[1.5,2]$. Is there a specific datastructure (or algorithm) for ...
0
votes
1answer
46 views

Which data structure contains of one parent node and many child nodes [closed]

I like to represent the following numbers in a data structure, like in trees or list but with one parent node and possibly many child nodes 1.3.1.1.0 1.3.1.1.1 1.3.1.1.2 1.3.1.2.0 ...
2
votes
2answers
62 views

Efficient Representation of (spatially sparse) spatial time series

Background I have a huge dataset consisting of points (on a plane) together with a timestamp for each point. This is a collection of car GPS measures, giving us the location (latitude/longitude) of ...
1
vote
1answer
128 views

How to handle 2D and 3D models efficiently

My coworkers and I have developed a c++ library implementing a "3D Geological Model" class. Goal of this library is to provide a data structure that is used in computational codes (such as Finite ...
2
votes
0answers
236 views

Algorithm for face based data-structure - CFD

Good morning I'm trying to develop an unstructured CFD code to solve Euler equations in a finite-volume (cell-centered) context (learning purposes). I was able to build from a cgns file some basic ...
1
vote
0answers
64 views

Data format for Cartesian mesh with cut cells

Is there a mesh data format which is particularly well suited for Cartesian meshes with Dey-Mittra style cut-cells? Ideally, one which does not require converting the cut-cells into a more general ...
6
votes
2answers
6k 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 ...
4
votes
3answers
214 views

K-nearest neighbours search in subspaces of a high-dimensional space

I'm looking for a good way to partition a large, fairly high-dimensional dataset in order to perform fast kNN searches not just in the full $N$-dimensional space, but also in lower-dimensional ...
3
votes
5answers
883 views

Algorithm for efficient weighted sampling from a collection that can efficiently be updated

I'm writing a Monte Carlo simulation in which I have to maintain a large collection of items. This collection contains a great many duplicates, and it will most likely be best to store some or all of ...
3
votes
2answers
409 views

data structures for efficient/easy implementation of finite volume method for 2D Poisson equation

My question is about implementation alone. Consider a square domain with regular square, cell centred finite volumes. This is for the multiscale finite volume method (Jenny and Lunati) I need to ...
2
votes
2answers
9k views

Implement the Huffman code in Python or Numpy?

The Huffman code is a way of compressing data streams by encoding the more frequent items with shorter words. Here is a distribution on the letters A thru J and the code I obtained: ...
7
votes
2answers
1k views

adaptive Gauss-Kronrod quadrature with vector-valued integrand

So I'm trying to implement a Gauss-Kronrod adaptive quadrature. That is, I want to calculate $$\int_a^b f(x) dx = \sum_i f(x_i) w_i$$ where f(x) is evaluated at multiple points at once for ...
1
vote
0answers
332 views

Practical implementation of spatial binning for rectangular range queries

I have a bunch of polygons and a coarse uniform grid. I want to implement two different range queries, for a rectangle aligned with the uniform grid: Does the rectangle intersect with any polygon at ...
1
vote
0answers
62 views

Minimum path in an undirected graph with 2 kinds of edges (locked and unlocked)

Given an undirected graph with positive weights, there are 2 kinds of edges: locked edges and unlocked edges. Determination if a given edge is either locked or unlocked edge takes O(1). For given ...
10
votes
2answers
1k views

Data structures for finite volume code: Arrays vs Classes

I have to write a finite volume code for Magnetohydrodynamics (MHD). I have written numerical code before but not at this scale. I just wanted to ask which will be a good choice, using a data ...
8
votes
2answers
2k views

Proper data-structure and algorithm for 3-D Delaunay triangulation

I have worked out some poor code to achieve the goal of 3D Delauney triangulation(random points in E3), but the time consuming is huge, and when five points are exactly (or nearly due to the round-off ...
14
votes
5answers
646 views

Repeated nearest neighbor calculation for millions of data points too slow

I have a dataset running into millions of data points in 3D. For the calculation I am doing, I need to calculate neighbor (range search) to each data point in a radius, try to fit a function, ...
5
votes
3answers
182 views

Where do I find data to start a graph data structure to practice on?

I am interested in learning firsthand about graph data structures but have no data to put into the database. Can anyone recommend a source for a beginner to find graph data? (Preferably a source that ...
12
votes
2answers
849 views

What are some good data-types for unstructured cell-centered FVM CFD code?

I'm interested in an advice for efficient data structures for cell browsing in unstructured cell-based finite volume CFD. One example that I encountered (in dolfyn cfd code) goes like this (I'll show ...
4
votes
2answers
2k views

Extracting a 2D matrix from a multidimensional array in C

In my c language program, I have to store multiple dense $m\times m$ matrices corresponding to gridpoints $x_i$ with $i=1,...,n$. I decided to create a three dimensional array $A\in R^{n\times m\...
5
votes
3answers
244 views

How to efficiently structure simulation data in memory for cells with varying degrees of freedom?

For a discontinuous Galerkin-based simulation I need to store cell-based simulation data in memory. Since the order of the polynomial approximation $N_p$ may vary between cells, I wonder what the most ...