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19 views

Calling scipy.integrate.odeint, solve_ivp, or any possible python solver in matlab

Do you know any way to call scipy.integrate.odeint, solve_ivp, or any python solver directly within a Matlab code? I have tried ...
0
votes
1answer
39 views

Compute 1st derivative with backward difference approximation in python

I am trying to write a function to compute 1st derivative with backward difference approximation. $ u'(x_i) = \frac{u(x_i) - u(x_i - \Delta_x)}{\Delta x} \equiv D_- u(x_i).$ And for the first point, ...
7
votes
4answers
18k views

Plot integral function with scipy and matplotlib

I want to plot a numerical integral function of some function $f$ using scipy and matplotlib. How can I do this? I tried the ...
3
votes
1answer
638 views

Interpolation using compactly supported radial basis function

I have been struggling for two days with the following problem. I would like to do a $d$-dimensional interpolation over some data. I tried first to use polyharmonic splines, but when the size of data ...
1
vote
0answers
20 views

Understand the need for Welford's online algorithm

I am puzzled by the Wikipedia entry discussing many online algorithms for computing the sample variance, including the Welford's online algorithm. In particular, the sample variance $s_n^2$ can be ...
-1
votes
0answers
19 views

What is the issue with my Code here? [closed]

I am trying to read in a CSV file for one of my boundary condition in OpenFoam, but for some reason OpenFoam is not reading the file. There is no error message or anything, it just not showing the ...
4
votes
1answer
45 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(...
1
vote
1answer
42 views

Matlab - Compute approximative common eigenvectors between two matrices as a function of tolerance

I am looking for finding or rather building common eigenvectors matrix X between 2 matrices A and B such as : ...
0
votes
1answer
40 views

Technique to find the CFL condition using the Galerkin method in space and finite-difference in time?

I am using the Galerkin method (Discontinuous to be precise) to discretize in space the scalar linear wave equation and the explicit second order centered finite difference scheme to discretize in ...
12
votes
3answers
452 views

What guidelines should I follow for simulation software projects?

I am not sure whether this question belongs here, but I would like to give it a try and benefit from the experience of the people at scicomp.SE. From my experience, the software quality in ...
7
votes
1answer
556 views

full rank update to cholesky decomposition for multivariate normal distribution

This question is a specialization of full rank update to cholesky decomposition, to which I hope to get a more positive answer. When calculating the minus log of the multivariate normal distribution, ...
1
vote
0answers
29 views

Integrating a wavelike equation with absorbing boundary conditions

I am trying to numerically solve the following equation: $\frac{\partial^{2} \phi}{\partial t^{2}}-\frac{\partial^{2} \phi}{\partial x^{2}}+V(x) \phi(x, t)=0$ On some domain, with: $\phi(x, 0) = I(x)$ ...
1
vote
1answer
49 views

Gauss Integration of $\sqrt(x)$

I want to construct a gauss integration for the weight function $w(x) = x^{1/2}$ for $$\int_{0}^{1}x^{1/2}f(x)dx = a_{1}f(x_{1})+a_{2}f(x_{2})$$ Solving \begin{align*} a_{1}+a_{2} =& \int_{0}^{...
1
vote
0answers
37 views

3D Matrix (Tensor) Operating On a 1D Vector

Say you have a tensor $T$ and the components are represented by a 3 by 3 by 3 matrix. And you want to use that tensor to map a vector $u$ into a new vector $s$, both of which are 3 by 1 column vectors....
5
votes
1answer
90 views

Solving PDEs in parallel

I have read different approaches on how to solve pdes in parallel which are discretized using finite element method. For example: Non-overlapping domain decomposition approach as mentioned in https://...
2
votes
0answers
115 views

Parametric nonlinear programming

I believe, I have a parametric nonlinear optimization problem. The non-convex constraints depend on some parameters, and I seek a solution that satisfies these constraints for all parameters in a ...
7
votes
1answer
132 views

Which finite difference better approximates $uu'$?

I want to approximate $uu'$ with a finite difference. On the one hand, it seems to be $$(uu')_i=u_i\frac{u_{i+1}-u_{i-1}}{2\Delta t}=\frac{u_iu_{i+1}-u_iu_{i-1}}{2\Delta t}$$ On the other hand, $$(uu')...
-1
votes
0answers
18 views

Help in agglomerating a mesh with Metis?

I have got a mesh of triangles (for a finite element code) that I'd like to partition into polygons, much better if convex. I tried metis and it is very complicated but powerful if one knows about ...
-1
votes
0answers
18 views

Split classroom sizes in half linear integer programming

I work for a school who is looking to split students into two groups for COVID related reasons. Ultimately we need to split the students by class section and try to keep families to be in the same ...
0
votes
1answer
83 views

R function or package for carrying out maximum likelihood techniques in random effect models

I am applying optim() function in R to obtain maximum likelihood estimates of the fixed effects and random effects in a model with bivariate random effects. The ...
1
vote
1answer
76 views

Is there any way to have a better guess for initial condition of an ODE coupled to CFD as a boundary condition?

I'm doing CFD simulations for blood flow in unstructured grids. My boundary condition at the outlets is called three-element Windkessel which basically calculates the pressure by solving this ODE: $$...
2
votes
1answer
78 views

Efficiently compute a projection matrix from Householders reflectors

Let $A \in \mathbb{R}^{m \times n}$ where $m \geq n$. Let $B$ and $\tau$ be the result of applying LAPACK's dgeqrfp method (R on the upper right triangle, and the ...
5
votes
3answers
884 views

implicit vs. explicit domain decomposition methods

I've been working on a finite element code on unstructured methods, which I've parallelized using the Schur complement method. Here's a summary of how I did it: Assign each triangle of the mesh to a ...
3
votes
1answer
277 views

Givens rotation vs 2x2 Householder reflection

The usual story of Givens rotations vs Householder reflections is that Householder reflections are better if you want to map a long vector to $e_1$, while Givens is better if you want to map a 2-...
0
votes
1answer
42 views

Error too large in leapfrog method for solving the wave equation of a vibrating string

I have been trying to figure out what I did wrong for the last two days. I do not know if I actually did something wrong or if the error is supposed to be this large in usual leapfrog problems. I ...
1
vote
2answers
74 views

Efficient ODE steppers with query of $f$ and $\nabla f$ is efficient

Assume we have an IVP $y'(t) = f(t,y)$, and that $\partial_t f$ and $\nabla f$ are cheap to compute. Assume further that more derivatives are not cheap to compute, or inaccessible for some reason, ...
0
votes
0answers
49 views

Interpolation of a Concave Mesh

I would like to have an algorithm that interpolates the values attached to nodes in a concave mesh mesh. To be me precise, assume we have a point cloud P (e.g. in 3 dimensions) and a list of edges E ...
6
votes
2answers
788 views

How to properly calculate CPU and GPU FLOPS performance?

Problem I'm trying to calculate CPU / GPU FLOPS performance but I'm not sure if I'm doing it correctly. Let's say we have: A Kaby Lake CPU (clock: 2.8 GHz, cores: 4, threads: 8) A Pascal GPU (clock: ...
17
votes
2answers
1k views

Best practice for storing hierarchical simulation data

TL,DR What is the accepted best practice in scientific computing circles for storing large quantities of hierarchically structured data? For example, SQL does not play nicely with large sparse ...
1
vote
1answer
34 views

Finite element analysis software for acoustic and electrostatic

I need to do a simulation for my thesis project involving some piezoelectric nanoparticles in a fluid beamed with ultrasounds. I'm looking for a software for such simulation and for now it seems me ...
0
votes
1answer
46 views

Finite Element Analysis based on contractions of a subset of edges in enterior of mesh

I am modelling a problem that is "driven", not by typical boundary conditions but, by contractions in its interior. In a finite element analysis, I can specify the new lengths (not ...
0
votes
0answers
11 views

How to define "Characteristic length in Ansys CFX Power Syntax script?

I am trying to evaluate Reynolds number in Ansys CFX 2020 R2 using CCL/Perl script on different domains in a radial turbine. But for that, I need to define the Characteristic length. So I define the ...
0
votes
1answer
33 views

How can I compute the gradient of the noiseless image given by the compass operator?

I need to generate an image with 11x11 pixels having in the center of the image a square of 5x5 pixels, with the gray level of the background 0 and the gray level of the square is 50. I need to ...
0
votes
0answers
8 views

Different values of Gaussian Integration in Pracma library in R

I want to construct a gauss integration for the weight function: $$w(x) = x^{1/2}$$ $\in(0,1)$ of the form: $$\int_{0}^{1}x^{1/2}f(x)dx = w_{1}f(x_{1})+w_{2}f(x_{2})$$ \begin{align*} w_{1}+w_{2} =...
0
votes
1answer
340 views

Imposing periodic boundary condition for linear advection equation - Node problem

I've spent the whole day trying to figure out what is the correct way to impose (and implement) periodic boundary conditions $u(0,t)=u(1,t)$ for all $t>0$ for the simple advection equation $u_t + v ...
2
votes
1answer
62 views

How to include negative number in the log-sum-exp?

I want to know summation of some small numbers, such as {e^-1000, -e^1001, e^1002...} If all numbers are positive, I can use log-sum-exp algorithm. But unfortunately, negative numbers are also ...
0
votes
1answer
66 views

Smoothed Particle Hydrodynamics: Weird clustering of particles. Is that normal?

I implemented a rather simple SPH simulation using a cubic-spline-kernel and a simple non-iterative pressure solver as described in this PDF in equation 9. I followed algorithm 1 of that paper (...
0
votes
1answer
55 views

How to compute gradient of each node in finite element method?

I have a problem with computing gradient of each node in finite element method. I can get the value of each node. But how can I get the gradient? I know $u = \sum u_i \phi_i$ where $\phi_i$ are the ...
1
vote
0answers
31 views

N-body correct scaling

I realized an usual way to scale an N-body problem for an N-body simulation is by choosing units such that gravitational constant $G = 1$, but I'm probably doing it the wrong way. Suppose I simply ...
0
votes
0answers
24 views

Largest triangle that contains a point

Given the location of $n$ points on a 2D plane ($P_1, P_2, \ldots, P_n$); and the location of a special point $X$. Find three points $P_i,P_j,P_k$ ($i \neq j \neq k$) such that point $X$ is inside the ...
-1
votes
0answers
18 views

Is the corpus, on which the pre-training of BERT is based, being updated after its release in 2018? [closed]

Google's NLP language model BERT was pre-trained on the BooksCorpus comprising 1000M words (Zhu et al., 2015) and English Wikipedia comprising 2500M words (Devlin et al., 2018). Is the model being ...
-1
votes
0answers
30 views

Gmsh undesired behaviour 3D mesh

I would like to generate a 3D hexahedral mesh starting from a STL file using Gmsh 4.8.0. I followed these steps: Opened a STL file: file->open Added a volume: Modules -> Geometry -> ...
4
votes
1answer
109 views

Floating point and global error in Euler Method

Inspired by this answer, I tried to understand when floating point errors come into visibility and to check it also comparing the plot of the numerical solution with Explicit Euler with the analytical ...
-1
votes
0answers
24 views

Defacto Barnes Hut / N-Body MPI C implementation

I'm looking for a relatively straightforward but robust MPI-based parallel n-body application implementation in C/C++ -- ideally one that's off the shelf and has been used in other papers before. A ...
-1
votes
0answers
25 views

Is it ok to get the parameter of a random variable, from a random variable itself?

I want to generate the parameter, for a Poisson distribution, from a lognormal distribution. Has there been literature on if this is proper in probability & statistics, or are there nuances to ...
0
votes
1answer
86 views

Numerical solution of ill-conditioned differential equation

I want to solve the following Cauchy problem \begin{equation} y' = y^2 + \frac{t^4 - 6t^3 + 12t^2 - 14t + 9}{(1+t)^2} \end{equation} with initial condition: $y(0) = 2$ for $t \in [0,1.6]$ using a 3 ...
-1
votes
0answers
19 views

How could I find out how many FLOPs my calculator is capable of?

Looking at previous S.E answers, we have a formula for this: The theoretical peak FLOP/s is given by $$ \text{Number of Cores} * \text{Average frequency} * \text{Operations per cycle} $$ After ...
0
votes
0answers
27 views

Parameter sampling from a 3D isosurface in R

Before we start, a small disclaimer: I am not a computer scientist, and the field of isosurfaces is new to me, so hopefully, the question is phrased clearly:) Otherwise, let me know, and I will (try ...
0
votes
0answers
17 views

Boundary conditions inside a 3D domain with Thomas algorithm

I'm modelling the diffusion of molecular oxygen in a 3D domain by using as FDM Successive Over Relaxation (SOR) by lines. Oxygen concentration in each voxel should be found through a stationary PDE ...
0
votes
2answers
69 views

Problem of half-planes intersection

Consider the half-planes $\{x \leqslant 2\}$ and $\{x+y \leqslant 3\}$. These two half-planes are coded with the R package 'rcdd' as follows: ...

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