Questions tagged [numpy]

NumPy is the fundamental package for scientific computing with Python.

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19 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(...
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1answer
149 views

How to compare 2D vector fields and minimize the difference?

I want to compare the field of two electrical currents and compare the resulting field to a magnetic dipol field and find magnetic momentum that minimizes the difference of the two fields. My current ...
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0answers
58 views

Help with vectorized computation where vector multiplication would need to create an additional dimension

I want to use vectorized computation (with python and numpy) to do some calculation involving bessel functions. As is often the case, I need to calculate the sums of bessel functions of (infinit) ...
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2answers
63 views

The derivative of a gauss function via FFT and IFFT in Python

I have a problem with computing a derivative of a Gauss function using FFT and IFFT from NumPy library. I use the fact that $$ \begin{equation} \frac{d}{dx}f(x) = \frac{1}{\sqrt{2\pi}}\int{ike^{ikx}\...
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1answer
93 views

Help with modified bessel functions

I'm trying to parse the following expression (Eq. 35 in The Magnetic Field in the Vicinity of Parallel and Twisted Three-Wire Cable Carrying Balanced Three-Phased Current) in Python and calculate its ...
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0answers
17 views

Problem with recursive implementation of Subspace Iteration method in Numpy

I am having trouble with implementing the method of subspace iteration to find the eigenvalues and vectors of a random, symmetric matrix, A that is mxm with m = 10. ...
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1answer
48 views

Converting for loop from matlab to python

I am converting some MATLAB code in to python and have the encountered the error "ValueError Traceback (most recent call last) in 1 for ig in range(nbas): ---->...
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53 views

how can I plot specific iterations?

I have made this code for an explicit Euler method but I want to plot only the 0,1,25,50 iterations not all of them.How can I do it? ...
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1answer
55 views

Odeint error for nonlineal differential equations

I receive the following error when I run the code. ODEintWarning: Excess work done on this call (perhaps wrong Dfun type). Run with full_output = 1 to get quantitative information. warnings.warn(...
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0answers
104 views

How to take convolution of two arrays in Python by using NumPy?

Generally, we know that if we have this relation between Fourier transforms of three functions in frequency domain as: $$\mathfrak{F}\{\mathsf{P}(t)\} = \mathfrak{F}\{\mathsf{Z}(t)\}\mathfrak{F}\{\...
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1answer
78 views

Fast nonzero indices per row/column for (sparse) 2D numpy array

I am looking for the fastest way to obtain a list of the nonzero indices of a 2D array per row and per column. The following is a working piece of code: ...
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40 views

How to plot a function for multiple values of a parameter in the same set of axes in Python?

I'm currently trying to plot a graph wich describes a photoionization cross section as a function of incident photon energy for optical transition in a semiconductor for different values of the $\...
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1answer
107 views

Composite matrices in Numpy

Lets say I have four matrices A, B, C and D, and I want to combine them together into one new matrix for computation: $$ \left( \begin{matrix} A & B\\ C & D \end{matrix}\right) $$ How can I ...
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1answer
58 views

Best way to convert a sparse (containing zeros) covariance matrix into a correlation matrix?

I have a $100$x$100$ covariance matrix that looks like this. Some rows/cols are all-zero because those corresponding elements are not present in the sample from which covariance is calculated. I'm ...
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1answer
78 views

How do I find the portion of a cell/voxel lying within a defined surface?

We have a 3-dimensional grid of voxels (or cells), with individual voxels being of volume $dx\,dy\,dz$ where $dx=dy=dz=1$. A cone-like surface is defined by some function, $z = f(x, y)$, which in ...
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1answer
55 views

Numpys `tensordot` and what is happening mathematically

I've encountered a program where np.tensordot was used, so I tried looking it up but I can't really understand what this function is doing... I feel rather ...
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53 views

Why am I not getting the flat phase when Fourier-transform a Fourier-limited Gaussian pulse?

I have been trying to obtain a spectrum and a spectral phase of a Gaussian pulse using the Fast Fourier Transform provided with numpy library in Python. Here are ...
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2answers
213 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 ...
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1answer
89 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 (...
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1answer
155 views

Numerical stability in the product of many matrices

I have to calculate in numpy the matrix-product of many matrices (~400). Are there common practices to increase numerical stability? If this is relevant, the matrices are $300\times 300$ orthogonal ...
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0answers
75 views

Calculate integrals using numpy.fft

Good evening, I would like to understand why I do not get the correct result: I assume that I know my function on discrete data points and expand it as a discrete Fourier transform: $\text{sin}(x)=\...
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166 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 ...
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1answer
703 views

Numerical derivative in python

I am trying to take the numerical derivative of a dataset. My first attempt was to use the gradient function from numpy but in that case the graph of the derivative ...
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0answers
91 views

Smoothing FFT result

I am trying to calculate the spectrum of Bremmstrahlung, which involves calculating the Fourier transformed acceleration. I am solving a non-linear ODE to numerically calculate the acceleration in the ...
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0answers
207 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-...
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1answer
333 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, ...
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1answer
494 views

Implementing structured grid boundary conditions using NumPy arrays?

I am making a toy code in Python to solve the advection equation $$u_t + cu_x = 0$$ with, for example, periodic boundary conditions. Background information The numerical grid is specified like this: ...
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2answers
2k 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} & \...
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1answer
182 views

Doing computations on a very large numpy array: streaming the calculation vs out-of-core memory

I am trying to perform a calculation in numpy that depends on several parameters, and involved the creation of many intermediate arrays. These intermediate steps involve integrals over more parameters....
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1answer
60 views

numpy.outer without flatten

$x$ is an $N \times M$ matrix. $y$ is a $1 \times L$ vector. I want to return "outer product" between $x$ and $y$, let's call it $z$. z[n,m,l] = x[n,m] * y[l] ...
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2answers
307 views

Numpy FFT gives me a pulse shorter than it should be. Not sure what I am doing wrong

I've created a code (Python, numpy) that defines an ultrashort laser pulse in the frequency domain (pulse duration should be 4 fs), but when I perform the Fourier Transform using DFT, my pulse in the ...
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2answers
397 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:...
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1answer
85 views

Problem of multiplication of big (sparse) matrix with numpy (python)

I wanted to multiply two simple (big and sparse) matrix with numpy. And I saw that the calculation fails when matrices are too big. If i take $X$ a random vector (size $n$). With pandas, I ...
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1answer
66 views

Specifying mesh spacing for DFT in numpy

I was testing the .fft package of numpy 1.16.1 in Python 3.7.2. In particular I was trying to verify that the transform resembles the analytical one for: $$f(x) = \mathrm{exp}\left[-\left(\frac{x-5}{2}...
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1answer
101 views

Creating an Interpolation of a w = f(x,y,z) function

I am trying to finish a series of interpolation functions. The problem is more related with organizing the data than how to do the interpolations. Using the RegularGridInterpolator, I created this ...
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1answer
995 views

Problems with python's interp 2D

I am writing some functions to interpolate data. While using interp2D, somehow, a sample matrix works but when I change the size of the matrix, it returns an error. ...
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1answer
73 views

Minimizing the used memory in diffusion simulation using Python

I am recently dealing with a diffusion simulation project and I have come up with the following code: ...
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1answer
5k views

Python Finite Difference Schemes for 1D Heat Equation: How to express for loop using numpy expression

Hello all, I've recently been introduced to Python and Numpy, and am still a beginner in applying it for numerical methods. I've been performing simple 1D diffusion computations. I suppose my ...
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1answer
98 views

Numpy: How to permute array into indices of larger array? [closed]

I have an array of length L with N zeros, and L-N non-zero values. I have another array of length N. I would like to put the values of the shorter array into the positions of the longer array which ...
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1answer
2k views

Applying neumann boundary conditions to diffusion equation solution in python [duplicate]

For the diffusion equation $$ \frac{\partial u(x,t)}{\partial t} = D \frac{\partial ^2 u(x,t)}{\partial x^2} + Cu(x,t) $$ with the boundary conditions $u(-\frac{L}{2},t)=u(\frac{L}{2},t)=0$ I've ...
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2answers
343 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 ...
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1answer
127 views

Is it possible to partition 2D data into bins such that each bin contains the same number of samples?

I am trying to sort data following a bivariate distribution into a numpy histogramdd, where each bin should contain the same number of data points (to the nearest whole sample). I expect that some ...
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568 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 ...
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0answers
88 views

Inconsistency in optimize.minimize

I am trying to fit a time-dependent curve at each time step. I do so in minimizing along $x_c$ the quadratic error between the curve and a reference solution $ 1/(1 + \exp\left(\sqrt{S}(x-x_c)\right) $...
3
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1answer
59 views

why am I not getting a staircase for the rotation number?

I'm trying to understand the staircase map. Look at this map from the circle to itself: $$ x \stackrel{F}{\mapsto} \big[\omega + x + \tfrac{\epsilon}{2\pi} \sin (2\pi x) \big] \pmod 1 $$ Such a map ...
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1answer
3k views

Why `import numpy as np` for scientific computing? [closed]

Why do scientists bother with the np for numpy? (Note this is more a "philosophical"/reasoning question - let us assume that ...
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0answers
107 views

computing dual matrix trace norm and tensor gradient in python

I'm trying to write the following function in python: $$ f_\mu(\mathcal X) = f_0(\mathcal X) + \sum_{i = 1}^n \max_{||\mathcal Y_{i(i)}|| \leq1} \alpha_i\langle \mathcal X_{(i)},\mathcal Y_{i(i)} \...
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1answer
317 views

Performing a random walk on a lattice that traps the particles

I am trying to solve this problem where we have a 1D-lattice of size 100 and the particle can start from any position in the lattice and moves randomly on it(with equal probability of moving to either ...
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0answers
228 views

Rank filter on an nXm array using python

I would like to apply a rank filter on an nXm numpy array. Let's say I have this array: ...
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1answer
2k views

Numpy.polyfit with regularization

I am trying to use the numpy polyfit method to add regularization to my solution. My non-regularized solution is ...