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0answers
68 views

Improve code of logarithmic quantizer

I am implementing a logarithmic quantizer which is defined as follows: $$ q(u) = \begin{cases} u_i , \frac{u_i}{1+\delta} < u < \frac{u_i}{1-\delta} \\ 0 , 0 \leq u \leq \frac{u_o}{1+\delta} \\ -...
5
votes
2answers
98 views

Optimizing a quadratic form integral over unit sphere

I have an optimization problem, which is to maximize the following integral over the unit sphere: $$ \max_B \int d\Omega \mathbf{f}^{\dagger}(\theta,\phi) (B^{\dagger} + B) \mathbf{f}(\theta,\phi) $$ ...
11
votes
2answers
230 views

Benchmark problems for eigenvalue reordering algorithms sought

Every real matrix $A$ can be reduce to real Schur form $T = U^T A U$ using an orthogonal similiary transform $U$. Here the matrix $T$ is quasi-triangular form with 1 by 1 or 2 by 2 blocks on the main ...
0
votes
2answers
109 views

Implementation of $[X, \cdot]$ as an $n^2 \times n^2$ matrix, where $X$ is an $n \times n$ matrix

Let $M_n(\mathbb{R})$ denote the set of $n\times n$ matrices with real entries. I have an $n\times n$ matrix $X\in M_n(\mathbb{R})$, and I would like to implement the linear operator $[X, \cdot] : M_n(...
2
votes
1answer
177 views

Double Integral with Gauss- Hermite for one component

I am trying to perform the following integral $$\int_{0}^{2\pi}\int_{0}^{+\infty} \frac{r'\left(e^{-r'^2/2\sigma^2}\right)\left(r-r'\cos(\theta-\theta')\right)}{r^2+r'^2-2rr'\cos(\theta-\theta')}dr'...
0
votes
1answer
299 views

Simple particle-in-cell examples

I am studying about the 1D EM-PIC (Electro Magnetics using particle-in-cell) simulation. I want to have a simultaneous time-integration of the electric/magnetic fields plus the motion of free charges ...
4
votes
3answers
540 views

FEM shape functions on triangular elements: transition from 2D to 3D

I'm writing a code for solving PDEs through the finite element method. In particular, I'm facing with 3D problems, in which I don't know how to calculate shape functions derivatives on the boundaries (...
0
votes
1answer
74 views

Looking for GPU support on Markov-chain Monte-Carlo (MCMC) codes

I am looking for MCMC codes with a GPU suport (like NVIDIA or OpenCL libraries) to make faster run chains. I know there is a plenty of codes that does MCMC but which ones could allow to exploit GPU ...
2
votes
1answer
173 views

Average value divergence in spectral method for Poisson equation

I'd like to know how to deal with a divergence when trying to solve the Poisson equation for electrostatics with a simple spectral method. I'm not sure how to best state my problem, so I'll explain ...
1
vote
0answers
28 views

Calculating the number of Flops of SPH density calculation

I would like to calculate the number of floating point operations (Flops) my code is performing in my machine. To do so, I would like to be sure I am counting the operations in the inner-most loop ...
2
votes
1answer
113 views

Developing a meshfree contouring algorithm

I would like to find the contours of a scalar function $u(x,y)$ available as a discrete set of function values $u_i = u(x_i,y_i)$ over a scattered set of points $(x_i,y_i), i=1,...,N$. In my case, the ...
3
votes
2answers
2k views

Applying the result of Cuthill-McKee in SciPy

I have applied SciPy's implementation of the Cuthill-McKee algorithm to a $48 \times 48$ sparse non-symmetric matrix in Compressed Sparse Row (CSR) format and the output is an array of length $48$ ...
2
votes
0answers
53 views

Variational loss of hp-Variational Physics Informed Neural Networks for 2D-Poisson Equation in Tensorflow

I am trying to reproduce the results from the hp-VPINN paper (https://arxiv.org/pdf/2003.05385.pdf) on tensorflow (v1) for Poisson's equation, particularly the two-dimensional Poisson equation. In one ...
1
vote
0answers
64 views

Attempt on 2d Advection with FDM - With Code

I tried to implement the 2d advection problem with a velocity field, that is not constant in space. My problem is, that the "mass" of my shifted density gets "eroded" or just ...
2
votes
1answer
160 views

How do I apply BDF2 in a STRANG splitting

I have a 3D diffusion equation that I want to solve using a time splitting (2D+1D). Assume that $A$ is the 2D discrete diffusion operator and $B$ is the 1D discrete diffusion operator. I want to use a ...
5
votes
1answer
774 views

Help with Fourier beam propagation method

I am working on implementing the Fourier beam propagation method in C++. I am really more of a programmer than a physicist but I think I have a good understanding of what I am trying to do. Here is ...
1
vote
1answer
90 views

What is the difference between Adittive Schwarz as a preprocessor and a solver?

As we all know, the Additive Schwarz approach can be used as either solver or preconditioner, however, my question is, what is the difference between the two? In other words, how to use AS as solver, ...
1
vote
1answer
96 views

2-norm and infinty norm of a system in controls

How to compute 2-norm or infinity norm of following system? i am confused whether to calculate using simple matrix theory "where it don't regard for s domain" or H2 and H-infinty norm. ...
4
votes
1answer
62 views

Stochastic cellular automata - algorithm limited by 1 cell per timestep

Context Let's say I am trying to model the spread of mold in a petri dish, using a stochastic cellular automata approach. The petri dish can be thought of as a grid of 1mm x 1mm squares, each called ...
3
votes
2answers
161 views

How to solve the integral-like energy equation with Sagdeev potential numerically in Python?

I am trying to numerically solve equation (6) of Lakhina 2021 in Python. The equation is $$\frac{1}{2}\left(\frac{d \phi}{d\xi}\right)^2 + S(\phi, M) = 0\, .$$ The Sagdeev potential expression is ...
-1
votes
1answer
140 views

Error in python (jupyter): index 1 is out of bounds for axis 0 with size 1 [closed]

I am an amature in python, I wrote a simple code in jupyter. But it is giving an error. I want to plot a function: ...
0
votes
0answers
58 views

Comparing minimas of two different functions

The goal is to find vectors $x_u$ and $y_i$, both of the same length $f=64$, and to do this the following loss function is minimized: $$\sum_{u, i} (1 + \alpha \cdot r_{ui})(p_{ui} - x_{u}^{T}y_i)^2$$ ...
1
vote
1answer
314 views

Lower bound for bilinear form in FEM

I'm searching for lower bounds of bilinear forms arising in FEM for elliptic second order PDEs with mixed boundaries. I did some research and found: $$\max_{v_{h}\in\mathcal{V}_h(\mathcal{\Omega})}a(...
1
vote
0answers
91 views

Weird "oscillatory" modes appearing in FEM simulations

I am using COMSOL to solve a mathematical model involving thermoelectric hydrodynamic (TEMHD) flow. I am running a very large parameter sweep and using the solutions obtained to make some plots. ...
1
vote
2answers
121 views

Need software for generating self-avoiding random walks on a tetrahedral lattice

I am looking for FOSS code that can generate self-avoiding random walk trajectories on a tetrahedral lattice. The purpose of the exercise is to create random conformations of model polymer chains that ...
0
votes
0answers
27 views

shifting mass along a vector field

I have a positive matrix $\rho \in \mathbb{R}^{n,n}_+$ as a discrete probability density. Furthermore, I have a tensor $u \in \mathbb{R}^{n,n,2}$ that is constant in time and acts as a vector field. I ...
8
votes
1answer
4k views

Computational methods for finding the energy eigenvalues of the time-independent Schrodinger equation with arbitrary potential

I have seen in some papers that the energy levels in some arbitrary potential are specified. How can one find the energy levels in such arbitrary potentials. For example, $V(x)=\sin^2(x/2)$ with $x\in[...
3
votes
2answers
918 views

Convergence problem for Poisson equation with periodic BC

I have written Poisson solvers using two different methods: A classic Jacobi scheme and one using the multigrid solver Hypre. I made up a couple of test cases ensuring the validity of those solvers. ...
4
votes
2answers
507 views

Difference between MoM and FEM

Method of Moments and Finite Element Methods are two of the most used methods in computational electromagnetics to solve electromagnetic equations. As it is known, in FEM sparse matrixes are used ...
4
votes
0answers
70 views

Global reconstruction defined elementwise in a-posteriori error estimator

This question is a follow-up of this previous one. In "Error Control for Discontinuous Galerkin Methods for First Order Hyperbolic Problems" by Georgoulis et al., an error estimator is ...
1
vote
1answer
253 views

Numerical solution of non-linear heat-diffusion PDE using the Crank-Nicolson Method

I am trying to solve numerically the following 1D EBM: $C\frac{\partial T[x,t] }{\partial t} - \frac{\partial }{\partial x}\left ( D(1-x^2)\frac{\partial T[x,t] }{\partial x} \right ) + I[T] = S[x,t](...
2
votes
1answer
79 views

Bounds for the optimal bandwidth of 2D/3D FEM stiffness matrices

is anyone here aware of whether there exist bounds on the optimal bandwidths of 2D/3D FEM stiffness matrices? Edit: more specifically, I would like to have bounds on the minimum bandwidth after ...
2
votes
1answer
67 views

Dividing a continuous domain into small squares; how to perform storage and querying?

I recently had a software engineering interview and was asked a series of questions that was a bit outside of knowledge realm, and I feel like there's some scientific computing principles here (I took ...
1
vote
1answer
71 views

What is the conventional approach for sparse matrix multiplication?

When you're multiplying sparse matrices against other sparse matrices or dense matrices, what is the conventional approach for each? How are the sparse matrices stored? What does matrix multiplication ...
18
votes
1answer
2k views

How to Run MPI-3.0 in shared memory mode like OpenMP

I am parallelizing code to numerically solve a 5 Dimensional population balance model. Currently I have a very good MPICH2 parallelized code in FORTRAN but as we increase parameter values the arrays ...
3
votes
4answers
142 views

Solving the eigenvalue from a set of coupled second order differential equation numerically

I met a problem in solving a set of coupled differential equation, as shown below: $$A_1\psi_1(z)+A_2\frac{d^2\psi_1(z)}{dz^2}+A_3\frac{d\psi_2(z)}{dz}=\lambda\psi_1(z)$$ $$A_4\psi_2(z)+A_5\frac{d^2\...
3
votes
1answer
81 views

Stability analysis simplification for PDE

I have the nonlinear PDE $$\frac{\partial U(z,t)}{\partial t} + A(U)\frac{\partial U(z,t)}{\partial z} + B(U)U(z,t) + C(z,t) = 0,$$ where $A(U)$ and $B(U)$ are guaranteed to be real and positive. I ...
0
votes
1answer
85 views

How is the integral of a projection over an element $T$ computed in practice? (deal.II related)

I'm studying an error estimator for the equation $\nabla\cdot(\beta u) + cu = f$ and it contains the following term $$||f - cU_h - \Pi(f-c U_h) ||_T$$ where : $\Pi$ is the local orthogonal $L^2$ ...
6
votes
1answer
185 views

Algorithm for solving systems which are nearly symmetric/adjoint?

I am familiar with Cholesky decomposition and LU factorization for solving systems of linear equations. I have a problem where I have large sparse matrices (say, 1000x1000 or larger) where only one or ...
0
votes
1answer
128 views

Why is Time evolving block decimation so efficient?

I have a short question about Time evolving block decimation (TEBD). During a lecture I was told that this method is very efficient in evolving 1D quantum spin systems with only nearest neighbor ...
1
vote
0answers
51 views

About the the stability of using an explicit scheme on the heat equation

Before I get to the heat equation I'd like to talk about the advection equation. Descritize that with FD in time and BD in space: \begin{equation} \dfrac{u^{n+1}_i - u^{n}_i}{\Delta t} + v \dfrac{u^{n}...
24
votes
8answers
5k views

Is it possible for user written algorithms to outperform libraries' built-in optimized functions?

I've always had this question in mind (even if it may sound vague), but in my numerical analysis courses we've always learned how to analyze and optimize code. However, since most linear algebra ...
3
votes
1answer
79 views

Type of computer used for computation

In some scientific papers I see that authors provide what type of simulation tool and what type of computer was used for computation. For example: The computations were performed using MATLAB in ...
0
votes
2answers
52 views

Basis function in a tetraedron for finite elements contex

In the finite element method we need to know a base for the fem spaces. For example, a base for the space $P_1(\hat{K})=<\{1-x-y,x,y,z\}>$ is a typical base for the polynomials of degree less ...
22
votes
5answers
10k views

Why are higher-order Runge–Kutta methods not used more often?

I was just curious as to why high-order (i.e. greater than 4) Runge–Kutta methods are almost never discussed/employed (at least to my knowledge). I understand it requires greater computational time ...
5
votes
2answers
183 views

Term for the typical "linear in the larger dimension, quadratic in the smaller" cost for linear algebra

Many dense linear algebra decompositions (QR, SVD...) on an $m\times n$ matrix have cost $$ O(\max(m,n)\min(m,n)^2) $$ when implemented in practice on a computer. Is there a colloquial name or a more ...
-1
votes
0answers
11 views

Nonlinear Integer programming (involving binomial calculations) with nonlinear constraints

I am working on a problem to distinguish between two binomial distributions. The resulting optimization problem is nonlinear and involves integer variables (number of binomial trials and number of ...
0
votes
2answers
44 views

Fortran: Can a procedure, contained in a module, call another procedure contained in the same module? [closed]

For instance, consider a module with the following general structure: ...
1
vote
2answers
145 views

Software and tutorial for FEM

i'm looking for some advice for finite element analisys. i'm a biomedical engineering student with few knowledge about the FEM. Tools like Comsol and Ansys are very powerfull but also complex and i ...
0
votes
1answer
102 views

Can someone help or point me out to C++ source code for a two body orbit simulation using symplectic integration?

I've professional experience with physics simulations and C++ programming, although I don't have specific experience with astrophysics simulations. I'm trying to build a two-body evolving system ...

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