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19
votes
1answer
2k views

Diagonal update of a symmetric positive definite matrix

$A$ is a $n \times n$ symmetric positive definite (SPD) sparse matrix. $G$ is a sparse diagonal matrix. $n$ is large ($n$ >10000) and the number of nonzeros in the $G$ is usually 100 ~ 1000. $A$ has ...
1
vote
1answer
47 views

Draw contour line to represent multiple contours

I have 5 data sets, each includes multiple scatter points. If I use the geom_path function in R, I could obtain 5 contours like the following graph shows. Those five contours are annotated outlines ...
0
votes
0answers
23 views

Truncated power series algebra implementation

1) I am looking for references for an efficient implementation and usage of TPSA. What sources exist besides Berz's 1989 original paper and the incomplete chapter in Dragt's book? 2) Are there ...
0
votes
0answers
42 views

What precautions should be taken when using 2D Perfectly Matched Layers?

I'm solving linearized Navier-Stokes equations with Perfectly Matched Layers in two spatial directions $x$ and $y$, but in the time-harmonic frequency $\omega$-domain, which is meant to be less ...
13
votes
2answers
3k views

Options for solving ODE systems on GPUs?

I would like to farm out solving systems of ODEs onto GPUs, in a 'trivially parallelisable' setting. For example, doing a sensitivity analysis with 512 different parameter sets. Ideally I want to do ...
2
votes
1answer
63 views

MATLAB's ode45 not dealing with initial conditions well [RESOLVED]

*Concern highlighted in yellow *Solution at bottom I have a differential equation to solve for the motion of an electron: $$ \frac{d^2v}{dt^2} = \frac{1}{\gamma^6}\left( \frac{eE}{\tau m} - \left( \...
1
vote
0answers
19 views

Using nondimensionalization to solve an ode in MATLAB [duplicate]

I am trying to solve an ode that uses some extremely large numbers and some extremely small numbers, namely $$ e = 1.6\times 10^{-19}\\ E = 10^6\\ \tau = 6\times 10^{-24}\\ m = 9.1\times 10^{-31}\\ c ...
2
votes
1answer
32 views

How to store all solutions of an ODE on Matlab for multiple values of a parameter

I would like to solve an ODE for multiple values of the parameter p and most importantly, save all the solutions for all the different values. Till now, I have ...
0
votes
1answer
70 views

How do I get power from gaussian beam numerically?

I would like to get the power from a Gaussian beam given a set of points at which electric field is evaluated. Please follow my reasoning and tell me what assumption maybe are wrong Power definition ...
1
vote
1answer
67 views

Why do not we choose the error solution norm as an iterative method's criterion?

For solving linear system $$ Ax=b, $$ using iterative mehods, we often use the terminate criterion as follows: $$ \frac{\|r_k\|}{\|r_0\|}=\frac{\|b-Ax_k\|}{\|b-Ax_0\|}<eps. $$where $x_0$ is the ...
3
votes
3answers
76 views

CPU usage when a MPI rank waits during a blocking communication

A typical way of dealing with I/O in MPI parallel programs is to either read all data to a single node and dispatch to the other nodes accordingly, or send all data to a single node and write from ...
1
vote
0answers
29 views

What kind of problem or matrices are suitable for multigrid method?

For Poisson or Convection-diffusion equation as follows: $$ -\Delta u=f,\qquad u|_\Omega = g. $$ or $$ -\Delta u +\vec{w}.\nabla u=f,\qquad u|_\Omega = g. $$ using FDM or FEM discretization, we can ...
-1
votes
1answer
20 views

Plot sinewave on ZX axis [duplicate]

I am trying to plot a sinewave with a bit of 3d perspective along the ZX axis instead of the XY axis. I have so far been unable to get anything that works, and have been unable to locate any examples....
0
votes
1answer
38 views

A lot of identical staff in Comsol material database?

I got a lot of elements in Material Browser of Comsol Multiphysics of Optics section. ...
0
votes
1answer
67 views

Solving differential equation in Python with discretized variable coefficients

I am trying to solve a differential equation with discretized variable coefficients which are calculated from a time serie. In this case the Runge-Kutta step size is fixed by the frequency in the time ...
1
vote
0answers
51 views

Using MATLAB to simulate the Ising Model

I am using MATLAB to simulate a 1D Ising Chain. I am running into an issue where when trying to find heat capacity, my system has a tremendous amount of noise. I'll post my code and an image of the ...
2
votes
0answers
27 views

Piecewise-linear Continuations vs Marching Squares/Cubes

It seems that both piecewise-linear continuation and marching squares are methods to produce iso-contours of a scalar function given the function's values on a grid. It seems that piecwise-linear ...
36
votes
11answers
2k views

Venues for publishing papers that emphasize software

Software is a fundamental part of computational science, and is increasingly recognized as an essential part of the scientific record. Given the value of using existing and well-tested code, it seems ...
5
votes
2answers
123 views

Is the diffusion equation with Neumann and Dirichlet BCs well-posed?

I am considering the following diffusion equation: $$\frac{\partial f}{\partial t} = \frac{\partial}{\partial x}[D(x,t)\frac{\partial f}{\partial x}]$$ over a grid ...
1
vote
0answers
39 views

Question regarding 1D implementation of the DG method

I'm pretty new to the DG method and have been writing a 1D code to help me understand the coding aspect. With respect a reference, I've been following these notes https://www3.nd.edu/~zxu2/...
2
votes
3answers
113 views

Is there any other sparse matrix data in matlab built-in file?

I want to do some numerical examples solving large sparse linear system Ax=b. And I want to use some data from Maltab itself because this experiments are easily ...
3
votes
1answer
143 views

Consumer hardware for scientific computing?

I'm interested in problems around probability, statistics, and statistical mechanics, and often I find it useful to perform simulations to get some sense of the underlying phenomena. Example ...
12
votes
3answers
542 views

Fitting Implicit Surfaces to Oriented Point Sets

I have a question regarding quadric fit to a set of points and corresponding normals (or equivalently, tangents). Fitting quadric surfaces to point data is well explored. Some works are as follows: ...
3
votes
0answers
65 views

Numerical integration with singularity term

In https://www.johndcook.com/blog/2012/02/21/care-and-treatment-of-singularities, the author explains the subtraction method to get rid of singularities when performing numerical integration. The ...
4
votes
1answer
67 views

Is operation count a reliable predictor of performance when comparing two formulations?

I have two formulations to solve a problem (both give dense, complex and symmetric system). They are solved multiple times in a loop. I am trying to predict which is better to use. The first one ...
0
votes
1answer
111 views

Why is modeling a physical system with ODEs sufficient?

I've read a few papers in dynamical systems where the model equations are sets of ODEs, with the state space, say, the spatial variables x, y, z, and an angle variable phi all evolving forward in time....
2
votes
1answer
95 views

What is eighth order central difference?

The origin of the question can be found here. I know the details about forward, backward and central differences. If $u$ is the variable, does eight order means it approximates the $u_{xx}$ using $u$...
0
votes
0answers
36 views

Why does the initial guess for linear system usually choose by zero vector?

For solving linear system $$ Ax=b, $$ using iterative mehods, we often use the terminate criterion as follows: $$ \frac{\|r_k\|}{\|r_0\|}=\frac{\|b-Ax_k\|}{\|b-Ax_0\|}<eps. $$where $x_0$ is the ...
2
votes
4answers
230 views

Role of weight function in Galerkin methods

I have difficulties in understanding the role of the weight function $w(x)$ that occurs in the solution of PDEs via the Galerkin approach. Consider a linear differential equation of the form $$ \...
1
vote
1answer
74 views

Crank-Nicholson for diffusion-advection vs diffusion equation

Let's consider the following 1D diffusion equation: $\frac{\partial u}{\partial t} = xk \frac{\partial}{\partial x}(\frac{1}{x}\frac{\partial u}{\partial x})$ where we assume that the diffusion ...
2
votes
1answer
53 views

How to set up a time-dependant matrix for an ODE to be solved using python?

I want to solve a problem numerically in python like this: $$ y(t)' = \mathbf{M}(t)y ,\\ y(0) = (1,0,0,0 ...) $$ where $y$ is an $n$-dimensional vector and $\mathbf{M}(t)$ is a time-dependant $n \...
1
vote
0answers
20 views

Fitting a multivariate PDE (using Java)

I'm doing simulations of 2 coupled PDE's with Comsol Multiphysics. I want to fit some data (using the Application method, whose language is Java) to those simulations. In order to answer my question ...
1
vote
0answers
33 views

How to use discrete cosine and discrete sine transforms in fftw

I work on fluid-related simulations. I have used FFT for fluid simulation. I want to use discrete cosine transform (DCT) and discrete sine transform (DST) to transform my velocity field to wavenumbers....
1
vote
0answers
36 views

FFT convolution works only with certain domain length

in my quest to understand how I can use FFT to compute integrals (see my other question click, still no answer there), I came across the fact that a convolution of two functions can be calculated by ...
12
votes
1answer
239 views

Algorithms for linear system of ODEs

I wonder: what is the best algorithm to solve \begin{equation} \frac{du}{dt} = Au \end{equation} Where $A$ is a real $n\times n$ matrix. A is not explicitly time-dependent, usually sparse but not ...
4
votes
2answers
264 views

Chebyshev and Legendre expansions

I am looking at approximating my function $f(x)$ using a Chebyshev and Legendre series and I ran into this question. Is interpolation using $n+1$ Chebyshev nodes the same as representing the ...
1
vote
0answers
11 views

How to use RODFT00 and REDFT00

I have some difficulty in implementing RODFT00 and REDFT00. I want to use them for fluid simulations. I would really appreciate ...
0
votes
0answers
33 views

DirichletBC definition on boundary subdomain for component of vector valued function in FEniCS

I am trying to impose a no-outflow condition for a velocity-field over a boundary sub-boundary domain in FEniCS. What I have find challenging is imposing the condition on a component of a vector-...
0
votes
1answer
39 views

Why PETSc/MPI uses only 1 processor a number of times, rather than using several as prescribed by mpiexec [closed]

I am a beginner to PETSc and MPI, so after installing PETSc I was compiling some basic tutorial. But whenever I give the number of processors i.e mpiexec -n 4 ./ex1 ...
6
votes
1answer
108 views

How fast is automatic differentiation?

I asked this question earlier on StackOverflow, but it's obviously better suited for SciComp: While there seem to be lots of references online which compare automatic differentiation methods and ...
6
votes
2answers
1k views

Runge-Kutta in the presence of an attractor

Suppose you are solving a system of equations numerically that possesses an attractor (no matter the initial conditions set, all the different solutions will approach a specific set of values that ...
0
votes
1answer
83 views

Robin Boundary Condition with Implicit Upwind - Finite Difference Method for 2D Convection-Diffusion Equation

I am trying to solve a problem with 2D Convection-Diffusion equation with U = Concentration ($mg/m^{2}$) using Implicit Upwind Finite Difference Method like this $$ \frac{\partial U}{\partial t} + ...
1
vote
0answers
67 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)=\...
0
votes
2answers
78 views

Is expm1 the right primitive?

I'm writing some code to calculate $\int_0^1 e^{ax} \mathrm{d} x$. Annoyingly there does not seem to be a way of doing this without if statements: ...
0
votes
1answer
51 views

How to implement Geometric Multigrid in non-rectangular grids?

It is quite easy to implement multigrid on a rectangular grid but what about an non-rectangular?How to coarse a non-rectangular grid and apply multigrid(assume an easy non-rectangular grid capital ...
3
votes
1answer
76 views

Dynamic linear elasticity problem is stiff (numerically)

I am considering a dynamic linear elasticity problem applied to a simple structure such as a beam. In system form, the PDE can be written as $M \ddot{X} + D \dot{X} + XK = F$ where $X$ represents the ...
2
votes
1answer
71 views

Lumped matrices in thermal analysis using finite elements

The governing equation of the transient heat transfer problem is $$C \frac{dT}{dt}+K T = Q$$ $C$ is the heat capacity matrix. $K$ is the thermal conductivity matrix. $T$ is the temperature vector. $...
3
votes
0answers
42 views

Subspaces for Iterative methods

In the original paper of Conjugate Gradients, the authors mention that if we pick the canonical basis $\{e_1,e_2,\ldots,e_n\}$, to obtain A-orthonormal vectors, we end up with the Gaussian elimination ...
2
votes
0answers
26 views

Fast approximate evaluation of Fourier-Legendre series

Suppose I know that a function from $[0,\pi] \to \mathbb{R}$ may be written as $$ \sum_{k=0}^\infty A_l \frac{2l+1}{4\pi} P_l(r) $$ where $A_l$ all are known. Is there a way in which I may very ...

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