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Questions tagged [numpy]

NumPy is the fundamental package for scientific computing with Python.

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31 votes
5 answers
30k views

Permute a matrix in-place in numpy

I want to modify a dense square transition matrix in-place by changing the order of several of its rows and columns, using python's numpy library. Mathematically this corresponds to pre-multiplying ...
none's user avatar
  • 508
20 votes
1 answer
3k views

How does the performance of Python/Numpy array operations scale with increasing array dimensions?

How do Python/Numpy arrays scale with increasing array dimensions? This is based on some behaviour I noticed while benchmarking Python code for this question: How to express this complicated ...
Nat Wilson's user avatar
18 votes
2 answers
15k views

Complexity of matrix inversion in numpy

I am solving differential equations that require to invert dense square matrices. This matrix inversion consumes the most of my computation time, so I was wondering if I am using the fastest algorithm ...
physicsGuy's user avatar
16 votes
1 answer
4k views

Why does SciPy eigsh() produce erroneous eigenvalues in case of harmonic oscillator?

I'm developing some larger code to perform eigenvalue computations of huge sparse matrices, in the context of computational physics. I test my routines against the simple harmonic oscillator in one ...
seb's user avatar
  • 994
14 votes
1 answer
2k views

Fast Automatic Differentiation for numpy?

I would like to use automatic differentiation to calculate gradients to function written in numpy. I've come across a number of packages, including autograd tangent chainer But none of them seem ...
user357269's user avatar
13 votes
3 answers
2k views

How to express this complicated expression using numpy slices

I wish to implement the following expression in Python: $$ x_i = \sum_{j=1}^{i-1}k_{i-j,j}a_{i-j}a_j, $$ where $x$ and $y$ are numpy arrays of size $n$, and $k$ is a numpy array of size $n\times n$. ...
N. Virgo's user avatar
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13 votes
1 answer
2k views

Can an approximated Jacobian with finite differences cause instability in the Newton method?

I have implemented a backward-Euler solver in python 3 (using numpy). For my own convenience and as an exercise, I also wrote a small function that computes a finite difference approximation of the ...
Stephen Bosch's user avatar
11 votes
5 answers
5k views

Memory efficient implementations of partial Singular Value Decompositions (SVD)

For model reduction, I want to compute the left singular vectors associated to the - say 20 - largest singular values of a matrix $A \in \mathbb R^{N,k}$, where $N\approx 10^6$ and $k\approx 10^3$. ...
Jan's user avatar
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10 votes
1 answer
334 views

Is it possible to express an arbitrary tensor contraction in terms of BLAS routines?

I noticed that libraries like numpy and pytorch are able to perform arbitrary tensor contractions at speeds similar to comparably sized matrix multiplications. This leads me to believe that underneath ...
ilya's user avatar
  • 111
9 votes
2 answers
897 views

Continuity of eigenvectors of parametric matrix

I have $n$-dimensional matrices $\mathrm{\hat{H}}(\vec{k})$ depending on vector parameter $\vec{k}$. Now, eigenvalue routines return eigenvalues in no particular order (they are usually sorted), but ...
tomic's user avatar
  • 91
9 votes
1 answer
1k views

Numerical integration for modelling curve for superconductors (Python)

I am a physicist who is trying to model the current-voltage characteristics of a superconductor-superconductor junction. The equation for this model is: \begin{align} I(V) = \frac{1}{eR_{\mathrm{n-n}...
query's user avatar
  • 91
8 votes
3 answers
12k views

Calculating partial trace of array in NumPy

A simulation I'm doing requires me to calculate the partial trace of a large density matrix. I am trying to calculate it using tools from numpy, but my code seems to be having some problems. For ...
msm's user avatar
  • 201
8 votes
3 answers
4k views

What does Python offer for distributed/parallel/GPU computing?

Using the SciPy/NumPy libraries, Python is a pretty cool and performing platform for scientific computing. I just wonder: When I have to go parallel (multi-thread, multi-core, multi-node, gpu), what ...
Michael's user avatar
  • 1,463
7 votes
3 answers
9k views

Can numpy.linalg.solve use back substitution when possible?

The question is if Python Numpy library can use back subsitution to solve Ax=b if possible, that is, if A is lower triangular? Do numerical linear algebra packages do this? I would think Numpy would ...
BBSysDyn's user avatar
  • 239
7 votes
3 answers
20k views

plotting discontinuous functions

I need help plotting the Heaviside function: Real analysis often involves constructing bizarre functions which are intuitively correct, but ultimately wrong. See the great book Counterexamples in ...
john mangual's user avatar
7 votes
0 answers
450 views

fastest way to compute many small dot products

I have two n-by-3 blocks contiguous in memory ("n vectors of length 3") and I'd like to compute the dot product between each of the rows as fast as possible. In numpy, using ...
Nico Schlömer's user avatar
6 votes
1 answer
3k views

Alternatives to numpy.einsum

Given an $n_1 \times \cdots \times n_k \times g \times g$ tensor $A$ (i.e. a collection of $g \times g$ matrices) and an $n_1 \times \cdots \times n_k \times g$ tensor $b$ (i.e. a collection of ...
Chris Swierczewski's user avatar
6 votes
2 answers
5k views

Is there an efficient way to form this block matrix with numpy or scipy?

Is there an efficient way to form this block matrix with numpy or scipy? $$ \left[ \begin{array}{cccc} \mathbf{B} & \mathbf{0} & \cdots & \mathbf{0}\\ \mathbf{AB} & \mathbf{B} & \...
drerD's user avatar
  • 161
6 votes
1 answer
499 views

roots of polynomials with small coefficients

I would like to compute the roots of a polynomial with exponentially small coefficients. $$ \sum_{n=0}^N a_n \frac{z^n}{\sqrt{n!}} \tag{$\ast$}$$ where $a_n$ are Normal random variables with mean $0$...
john mangual's user avatar
6 votes
2 answers
4k views

Using numpy arrays in Paraview programmable filter

How can I access a field in Paraview's programmable filter as a numpy array? I want to: Import an existing field as a numpy array Create a similar array for output Register it as a new field for ...
teekarna's user avatar
  • 231
6 votes
1 answer
461 views

Calculate large and small frequency separation for the Sun

I want to determine the big and small frequency seperation from timeseries data for the sun. An excerpt of the data (timeseries and power series) is plotted below. The power series is calculated in ...
user avatar
5 votes
2 answers
2k views

What algorithm(s) do numpy and scipy use to calculate matrix inverses?

I am solving differential equations that require inverting dense square matrices, and I wanted to know what algorithm(s) do numpy and scipy use to calculate matrix inverses?
kamy rez's user avatar
5 votes
1 answer
2k views

Rational functions in Python

I would like use Python to verify the following identities: $ \frac{1}{1-z} = 1 + z + z^2 + z^3 + \dots $ $ \frac{1}{1-z - z^2} = 1 + z + 2z^2 + 3z^3 + \dots $ $ q \prod_{n \geq 1} (1 - q^n)^{24} = ...
john mangual's user avatar
5 votes
2 answers
979 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
phlegmax's user avatar
  • 151
5 votes
1 answer
855 views

Stochastic SIR using SDEint python package

I want to use the SDEint package to give a numerical solution (plot) of the following stochastic SIR model. Namely, a system of SDEs. $$\begin{cases} dS = -\beta SIdt - \sigma SIdW \\ dI = (\beta SI -...
oliverjones's user avatar
5 votes
2 answers
553 views

Python: vectorizing a structured linear system solve

Overview I am looking for a way to solve a structured linear system in Python without using a for loop (preferably using vectorization, if possible). Background Consider the following linear system:...
Nathaniel Kroeger's user avatar
5 votes
1 answer
2k views

Sign differences in spectral decomposition in NumPy

I am trying to understand an example from a book, but I seem to get different answers depending on which spectral decomposition function I use in NumPy. I am trying to find a spectral decomposition $...
Flower-doctor's user avatar
5 votes
1 answer
1k views

Finite Volume Implementation

I am trying to implement a simple finite volume method solver. I had a class on FVM a while back, but am still aware of the principal concepts. But implementing the FVM for non-cartesian or 1D meshes ...
Markus's user avatar
  • 151
5 votes
1 answer
3k views

Logistic regression with Python

I am trying to code up logistic regression in Python using the SciPy fmin_bfgs function, but am running into some issues. I wrote functions for the logistic (...
tchakravarty's user avatar
5 votes
1 answer
250 views

How do I globally change the precision of a piece of code in Python to debug it?

I am solving a system of non-linear equations using the Newton-Raphson method in Python. This involves using the solve(Ax,b) function (...
Abel Thayil's user avatar
5 votes
0 answers
127 views

How to troubleshoot numerical instability using finite difference for steady-state non-linear heat conduction equation

I have a problem which I believe is numerical instability when trying to solve a heat conduction equation using finite difference. The short version is that when the parameter $I=80.3$ I get the blue ...
Ken Grimes's user avatar
5 votes
0 answers
193 views

Solving multiple linear regression in parallel

I am working on a problem where I need to solve approximately 500 Million Linear Regressions (OLS). What would be the most efficient way to do this (e.g. using GPU or a some framework that can do this ...
runtime's user avatar
  • 51
5 votes
0 answers
1k views

Python - calculation time derivative and laplacien by finite differences

I would like to determine a temporal derivative and a Laplacian by the finite differences method to solve the heat equation in a 1-dimensional case. My aim is to get the sources term that is why I ...
user3601754's user avatar
4 votes
2 answers
692 views

Fastest Way to Mutiply $10^4$ 2x2 Matrices

In a code that I work with (written in python, but also tagging as matlab because numpy is so close and I could use it if need be), we use a transfer matrix method to compute the properties of a ...
ElectronsAndStuff's user avatar
4 votes
1 answer
1k views

Poor SVD reconstruction of singular matrix

I am trying to calculate the singular value decomposition of this matrix using numpy.linalg.svd . However, reconstructing the matrix from the SVD gives a poor ...
myseun's user avatar
  • 53
4 votes
4 answers
11k views

LCM builtin in Python / Numpy

I can write a function to find LCM (lowest common multiple) of an array of integers, but I thought it must have been implemented in numpy or scipy and was expecting something like ...
Pagol's user avatar
  • 143
4 votes
2 answers
12k views

Consistent handling of division by zero in numpy array

I want to populate a numpy array with values from the smooth bump function f(x) = exp ( - 1 / (1 - x^2) ) if |x| < 1, f(x) = 0 otherwise Currently I ...
Willie Wong's user avatar
4 votes
1 answer
557 views

Going to try to move some of my scipy/numpy calculation to a new GPU, how to avoid disappointing results?

update: I've refactored the question based on helpful advice in the linked meta. I'm a heavy user of Python's NumPy and SciPy (and not much else) and for years I could run anything I need on my laptop....
uhoh's user avatar
  • 1,048
4 votes
1 answer
1k views

Diagonalize a unitary matrix with orthogonal matrices using numpy

An important component of the Cartan KAK decomposition for 2 qubit operations is to diagonalize a 4x4 unitary matrix using orthogonal (not unitary, purely real orthogonal) matrices. That is to say, ...
Craig Gidney's user avatar
4 votes
2 answers
678 views

Moore-Penrose pseudoinverse of singular rank degenerate matrix

I am trying to attain the Moore-Penrose pseudoinverse of a very large, very sparse, rank-degenerate, singular, and square matrix. ($75000 \times 75000$, near rank). The matrix is a graph Laplacian and ...
feik's user avatar
  • 143
4 votes
1 answer
2k views

Python syntax for MATLAB/Octave colon operator a:dx:b

I am trying to rewrite some MATLAB/Octave code in Python, and I don't know what would be the nicest or most intuitive way of writing ...
user avatar
4 votes
1 answer
858 views

Backwards Difference Implicit Method for Nonlinear Parabolic PDE in Python

Original Stack Overflow Question: https://stackoverflow.com/questions/65683788/indexerror-index-31-is-out-of-bounds-for-axis-1-with-size-31?noredirect=1#comment116218335_65683788 PDE: u_t = u_xx + u(...
AlphaArgonian's user avatar
4 votes
1 answer
1k views

Chebyshev approximation by projection vs interpolation

Suppose we want to approximate a function $f: [a, b] \rightarrow \Re$ with a Chebyshev series: $$ f(x) \approx \sum_{k=0}^n c_k \, T_k\left( \frac{2x-b-a}{b-a} \right) $$ where $T_k(x) = \cos(k\, \...
visitor's user avatar
  • 161
4 votes
2 answers
113 views

How to read the number of periods of this complicated graph?

I have two data sets that are quasi-periodic. They have the same period and can be seen clearly by eye. For example when $x\in(100,200)$, both of them have about 32 periods. Below is a zoom-in of the ...
an offer can't refuse's user avatar
4 votes
0 answers
177 views

How amenable is this 2D Frenkel–Kontorova-like energy minimization problem in Python to the use of a modest PC + GPU? (Heavy reliance on indexing)

@Richard's answer to Going to try to move some of my scipy/numpy calculation to a new GPU, how to avoid disappointing results? is quite helpful, and as promised I've added a simple running example ...
uhoh's user avatar
  • 1,048
4 votes
0 answers
768 views

What algorithm do BLAS and ATLAS use for matrix multiplication?

I have searched and what I understood was that they use the naive one with several memory and cache optimizations. However, I wanted to know whether they are using the Strassen or the Coppersmith-...
bedo dan's user avatar
4 votes
1 answer
2k views

Analytic solution 2D scalar wave equation in cylindrical coordinates numerical implementation

I am trying to compare my finite difference's solution of the scalar (or simple acoustic) wave equation with an analytic solution. For that purpose I am using the following analytic solution ...
imbr's user avatar
  • 366
3 votes
1 answer
773 views

Time and memory required to diagonalize a 18000 by 18000 matrix using numpy in python

Can someone give an estimate of the Time and memory required to diagonalize a 20000 by 20000 complex hermitian matrix using numpy in python ?
Snpr_Physics's user avatar
3 votes
1 answer
243 views

High frequency noise at solving diffusion equation

I'm trying to simulate a simple diffusion based on Fick's 2nd law. ...
sonium's user avatar
  • 133
3 votes
3 answers
9k views

Runge-Kutta Simulation For Projectile Motion With Drag

I am attempting to simulate projectile flight with drag. However, with a timestep of 0.1 seconds, I am consistently getting an error of ~0.1-1%. ...
Chronum's user avatar
  • 311