Questions tagged [python]
A general purpose high-level programming language that emphasizes ease of code syntax and readability.
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Heat Equation for fast source with FiPy
I'm trying to solve the following differential equation with FiPy, basically laser irradiation on a surface
$$
\rho_{s}C_{p,s}\frac{\partial T}{\partial t} = k_{s}\frac{\partial^{2}T}{\partial x^{2}} +...
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How to solve three coupled differential equations in python using RK-4 and shooting method? or using solve_bvp?
I am trying to solve three coupled differential equations in Python. I am using RK-4 techniques with Shooting method. I am trying to plot the f and N functions.
...
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Use of scipy.linalg.cython_lapack.dgbsv in cython script
I was working into accellerating a solver for baded matrix using cython.
The base case is the following pure python code :
...
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Efficient Solver for Solving a Large Linear System Sequentially of a Positive Definite Matrix
In my case, I am solving $AX=B$ repeatedly, but the solution usually doesn't change much. So it'd probably be faster than me when I start from the previous solution and iterative, rather than solving ...
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Preconditioner Implementation with matrix-free methods (sparse iterative solvers)
How can I define preconditioners (SPILU, SPAI, etc.) for sparse iterative methods (TFQMR, GMRES, CGS, etc.) for the matrix-free left-hand side? I defined $Ax=b$ using matrix-free $A$ (with ...
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Overflows and underflows in Python
I’m writing some Python code using NumPy. Since I got an overflow warning, I decided to check for underflows as well at all places in the code, using ...
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Coupled Partial Differential Equations
I'm trying to solve the following system of coupled differential equations, the two-temperature model for $e$ = electrons and $l$ = lattice.
$$
\rho_{e}C_{p,e}\frac{\partial T_{e}}{\partial t} = k_{e}\...
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optimize this python code that involves matrix inversion
So I have this line of code that involves a matrix inversion
X = A @ B @ np.linalg.pinv(S)
$A$ is an $n$ by $n$ matrix, $B$ is an $n$ by $m$ matrix and $S$ is an $...
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How can I efficiently find an anti-symmetric generator of a special orthogonal matrix?
Given a special orthogonal matrix $O$ (i.e: $OO^T = 1$ and $\det(O) = 1$), I am trying to efficiently find a matrix $X$ such that $O = e^X$ and $X = -X^T$ using Python (NumPy & SciPy).
One obvious ...
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What is the most accurate way of computing the evaluation time of a neural network model?
I am training some neural networks in pytorch to use as an embedded surrogate model. Since I am testing various architectures, I want to compare the accuracy of each one, but I am also interested in ...
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Coding a performant flexible scientific code with Python
I aim to code a PDE flexible fast PDE solver. I read and noticed multiple approaches:
Python + Numba
Python + Cython
Python + some compiled language (c++/fortran)
The equations to be solved are ...
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Help needed in generating a list of radii
I am trying to generate a list of radii between two given points (0 and 1 in this example). Below is my code in Python to generate the list.
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Why is Magnetic Susceptibility not showing the expected transition in 2D&3D Ising Model?
I'm trying to code the Ising Model with the metropolis algorithm to study the ferromagnetic-paramagnetic transitions. The code seems to work ; the equilibration happens. While equilibrating, the ...
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How to constraint the tangential gradient on a boundary in FEniCS?
The problem I'm considering is a 2D scalar PDE.
The domain $\Omega$ is a disk with two holes $\partial\Omega_1$ and $\partial\Omega_2$ and an external boundary $\partial\Omega_0$.
The PDE and boundary ...
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1
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Numerically solving the Advection-diffusion equation with no-flux boundary condition leads to violation of mass conservation
I am trying to solve numerically the advection-diffusion equation of the following form
$$\frac{\partial C}{\partial t}=\alpha\frac{\partial^2 C}{\partial x^2}+\beta \frac{\partial C}{\partial x}$$
...
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Find peaks method for finding elusive peaks
I'm currently utilizing the find_peaks function to identify peaks within this spectrum. However, despite consulting similar queries on Stack Overflow, my attempts to incorporate features such as ...
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How to calculate the numerical integration and plot the result in python?
I am trying to solve the question below in McQuarrie Physical-Chemistry book.
The first step of the exercise, I solved. However, the second step involves a numerical integration. I can develop a code ...
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Converting an expression into an einsum
I have the following expression that I need to calculate for some matrices:
$$
\sum_{k}c_{t,i,k}\sigma^\prime\left(w_tX_t+b_t\right)_k\left(\sum_\ell w_{t,k,\ell}\tilde{X}_t^{w,\ell}\right)
$$
I could,...
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BSplines from scipy not defined on whole range of the knots
I am looking at the construction of BSplines out of curiosity. I created a small code that uses scipy.interpolate.BSpline to create basic splines. I get the following basic splines for order 0, 1 and ...
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Auto differentiation with JAX in python and ForwardDiff.jl in Julia give matrices with different values but same structure. Are the results right?
Using ForwardDiff in Julia gives me the following values for 2 matrices
I have tried to use JAX to auto differentiate the same function in Python but I am getting
the following results for A and B ...
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97
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How to solve this nonconvex problem in python
I have the following problem to solve
minimize $$\sum_{i=1}^I\sum_{k=1}^Kx_{i,k}.$$
The constraints are as follows:
$$\sum_{i=1}^I\sum_{j=1}^J\ln(c+x_{i,k}A_{i,j,k})\geqslant B_k,\forall k,$$ and
$$\...
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Using multiple bounds constraints parameters for a convolved gaussian fit
I'm currently analyzing XRF spectra, specifically focusing on the spectrum of (Pb). In XRF spectroscopy, the lines in the spectrum can often be effectively modeled by Gaussian distributions. Here, ...
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241
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Converting large .tif files to zarr arrays
I have multiple .tif files which range from 500MB - 5GB. I need to convert them to zarr arrays and preferably write them to my disk. I have an aws ec2 linux instance with 32GB RAM. I have searched ...
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87
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First and second component of fft for circle approximation to periodic curve
I wanted to understand how the fast fourier transform work in numpy and for this I tried apply it on $n$ points of an ellipse $t_k = \frac{2\pi}{n-1}k$ with $k=1...n$ $$f_k = f(t_k) = (acos(t_k), bsin(...
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Parallel vs Serial computing using Python Qutip. Why is serial faster?
I am trying to learn parallel computing using qutip's parallel_map function. I've tried to write a basic and simple code to understand the differences between parallel and serial calculation of ...
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Calculating a 2D Ewald sum for a multipolar expansion
I am attempting to calculate the potential of a particle at the center of an infinite two-dimensional lattice as per the following reference:
Reference: Lambin, PH & Senet, P. Ewald Summation of ...
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125
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Different Results for Double Pendulum
In this study, (Hidden Fractals in the Dynamics of the Compound Double Pendulum) the authors provide various fliptime fractals (of a double pendulum) for different length combinations. However, when I ...
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Help in solving Quintessential scalar field using Steep Potential in cosmology
I am attempting to solve the differential equation $\ddot\phi + 3H\dot\phi + \dfrac{dV}{d\phi} = 0.$
For $V(\phi) = V_{0}e^{-\lambda\phi}$, where $V_{0} = 0.7$, $\lambda = 0.1$ and $V'(\phi) = \dfrac{...
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Is the following the correct implementation of VGG network?
As exercise I am implementing few fundamental networks.
Specifically right now I am implementing VGG
The code I've got at the moment is the following:
class MyVGG(nn.Module):
...
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How to simulate a multi propagation of a laser beam in atmospheric turbulence?
I want to simulate how a Gaussian beam would look like at the receiver plane when propagated through an atmospheric turbulence. For this I am using AO package. Since I didn't see any function for ...
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Difference of tensors to construct a higher dimensional tensor in pytorch
Suppose I have two tensors $A_{i_1,\ldots,i_M}$ and $B_{j_1,\ldots,j_N}$ where $M \neq N$ in general. We can define a tensor $C_{i_1,\ldots,i_M,j_1,\ldots,j_N}$ by
$$
C_{i_1,\ldots,i_M,j_1,\ldots,j_N} ...
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How to implement the following operation in pytorch (tensor by equating indices)
I wasn't sure if I should post this on stackoverflow rather than here, but because I have to construct a specific tensor I think here is more suitable.
I have 2 tensors, $x \in \mathbb{R}^{M \times N \...
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Efficient sum of distributions (mixture distribution) and sampling
I manage to implement adaptive sampling by drawing samples iteratively from an update distribution which is represented by a mixture of two distributions, such that
$$ρ_{new} = a * ρ_{old} + (1 - a) * ...
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Regarding the difference between Metropolis-Hastings and Wolff algorithm (synchronous vs asynchronous) applied to Ising Model?
I am trying to self-learn concepts at the intersection of physics and programming. When reading up on the Ising Model, I find that the typical programming tutorial (such as this one) covers the ...
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Solving a system of non-linear equations to find relationship between arguments
I have a program that implements a multivariate function, call it $f = \mathcal{Q}(Z,v)$ that I can compute given $Z,v$. The $v$ variable is related to the $f$ variable by another relation, call it $v ...
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optimizing piecewise linear objective functions (perhaps non convex) with equality constraints
When I do my project, I need to optimize piecewise linear objective functions (perhaps non convex) with equality constraints.
The piecewise linear objective function may be not convex like this in the ...
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Solving a polynomial with NumPy
I'm trying to do something that I thought would be very straightforward but somehow I'm struggling.
I have a time series and I want to extrapolate it, assuming a linear trend, to forecast when will it ...
user782
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How to minimize a numerical integration in python?
I need some help to minimize a numerical integration. It's about a classical problem in physics (hydrogen atom). It can be solved analytically but I need to solve it numerically in Python.
We have an ...
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I am currently working on a data ana that involves examining trends across 14 var. These var have distinct scales, making visualization a bit diff
Scaling Issues: Many of the columns I'm analyzing are in different scales, which makes it challenging to visualize them together effectively.
Visual Representation: I initially attempted to use ...
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Singular Matrix Error in Incomplete LU Decomposition
I’m currently working on solving the following PDE:
$$\begin{equation}
-(\mu_x \frac{\partial^2 u}{\partial x^2} + \mu_y \frac{\partial^2 u}{\partial y^2}) = f(x, y)\end{equation}$$
Where a right hand ...
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Numerical solution for inviscid Burgers' equation seems to have no breaking time?
So I'm trying to use the Lax-Friedrichs method to solve the inviscid burgers' equation with initial condition $$u(x,0) = \sin(x)$$, using
$$u_m^{n+1} = \frac{1}{2}(u_{m+1}^n + u_{m-1}^n) - \frac{\...
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Solving AU = F using linalg.cg results in 0 iterations
I am working on solving the following PDE: $$\left(\mu_{x}\frac{\partial^{2}u}{\partial x^{2}}+\mu_{y}\frac{\partial^{2}u}{\partial y^{2}}\right)=f(x,y) \tag 1$$
Which is then discretised:
$$- \mu_{x} ...
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Numerically computing envelope of Gibbs oscillation
If I numerically compute the envelope of $\sin(\pi t)$ using a Hilbert transform, I obtain exactly what I expect:
If I do the same for $\mathrm{sinc}(t)$, still I obtain an envelope which agrees with ...
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Large set of nonlinear equations in Sympy
I have a set of 6 nonlinear equations, and using Sympy I find the values of the 6 unknowns. This works perfectly and it directly gives the exact solution, using sympy.solve to be specific. Now I ...
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Solving non-linear partial differential equation numerically: $u_{xx}+u_{yy}=\mathrm{e}^{u}$
To start with, I need to solve this partial equation numerically, but I do not know how to do that. If I try a finite difference method, I face a problem that $u_{i,j}$ is also located in exponential, ...
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Numerical integration in Fourier space over 3D grid
I am attempting to implement a model outlined in this paper:
General magnetostatic shape–shape interactions
Background
This model allows the calculation of magnetostatic interaction energies between ...
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Implementation of operator splitting method for Wigner equation
I am dealing with the integro-differential equation for Wigner function,
$$\frac{\partial f}{\partial t}+p\frac{\partial f}{\partial x}+\\+\frac{1}{\chi}\left\{\int_{-\pi}^{+\pi}dy\,\int_{-\infty}^{+\...
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Does anyone know how to add a forcing term at the center of a cicular membrane?
I am here once again searching for wisdom, as some of you might notice I asked a related question a few days ago. And now I am struggling to add a forcing term at the center of the membrane, in order ...
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1
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Need help with the python code: Calculating Madelung constant CsCl crystal structure
Need help with the code to estimate the Madelung constant for CsCl lattice:
Cs at (0,0,0)
Cl at (0.5, 0.5, 0.5)
Answer: Converged value I am getting is 0.465. ...
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213
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Solving the wave equation for a circular membrane in polar cordinates
As you see this mode is not right, unless for what i understand
And the initial conditions were
...
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