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14 votes
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Sequential approach to solving coupled PDEs

I'm dealing with a coupled system of three transient, non-linear convection-diffusion equations. Let's just say to simplify the problem that they take the following form: $$ -\nabla\cdot(D_{1}(u_{2},...
Justin Dong's user avatar
14 votes
0 answers
446 views

Operator Splitting methods for DAEs

After doing some research, I've found that most of the literature on operator splitting methods (e.g. Strang Splitting, Fractional Step, etc.) are specifically designed for a standard problem type of ...
Paul's user avatar
  • 12k
13 votes
0 answers
713 views

Fast Eigenvalue and SVD Solver for Structured Matrices

I am looking for a fast Eigenvalue and SVD solver for small dense structured matrices (Hankel and Toeplitz). I have searched for efficient implementations in libraries like MKL but I am not able to ...
Sai Venkat's user avatar
12 votes
0 answers
4k views

Optimized open source BLAS / LAPACK package

I was wondering what is a more optimized open source BLAS/LAPACK package with respect to modern multi-core processors (Haswell and beyond). Is there any distribution that can attain performance close ...
tamumiket's user avatar
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12 votes
0 answers
138 views

Are there any standardized file formats for point group character tables?

Character tables are an important tool for symmetry analysis in many computational chemistry software packages. Are there any standardized file formats for point group character tables? This may seem ...
jvtrudel's user avatar
  • 221
10 votes
0 answers
335 views

Numerical integration using interval arithmetic, nowadays

Is there now a package for rigorous numerical integration that uses interval arithmetic and has access to a well-developed library of special functions? By "well-developed", I mean something that, at ...
H A Helfgott's user avatar
10 votes
0 answers
860 views

Implementing std::nextafter: Should denormals-are-zero mode affect it? If so, how?

This might be the wrong stackexchange site for this question. math.SE, cs.SE, programmers.SE, and of course stackoverflow are all possibilities. I'm hoping to reach an audience that might actually ...
Peter Cordes's user avatar
10 votes
0 answers
234 views

Time advance in Adaptive Mesh Refinement method

I am working on solving complex system of 2D PDEs governing the behaviour of plasma in a gas lamp during discharge. Recent tests have shown that because of steep gradients in temperature field and ...
Dantragof's user avatar
  • 131
9 votes
0 answers
233 views

Imbalance of variables in Mixing Newton's method and Linear solver for a Non-linear system

Problem Solving a non-linear system of equations. The number of variables is the same as the number of equations. When I fix a set of variables (say $\vec{y}$) and keep another set free (say $\vec{...
R zu's user avatar
  • 163
9 votes
0 answers
141 views

Review of modern homotopy methods and practical techniques

I'm hoping someone can recommend recent literature concerning homotopy methods for solving systems of nonlinear equations. Already by the time of Layne Watson's 1986 paper there were a lot of methods,...
OskarM's user avatar
  • 297
9 votes
0 answers
297 views

Wanted: sequences of linear systems for recycling Krylov solver analysis

In the solution of sequences of linear systems $$A_ix_i=b_i\quad\text{for}\quad i=1,2,\dots$$ with Krylov subspace methods, data can be recycled from already solved linear systems in order to speed up ...
andrenarchy's user avatar
9 votes
0 answers
527 views

Updating matrix diagonal with Woodbury matrix identity and maintaining numerical accuracy

I have a dense matrix A and its corresponding inverse $A^{-1}$. The Woodbury matrix identity states: $$ (A + UCV)^{-1} = A^{-1} - A^{-1}U(C^{-1} + VA^{-1}U)^{-1}VA^{-1} $$ I wish to perform small ...
Costis's user avatar
  • 1,320
9 votes
0 answers
432 views

Simple turbulence model appropriate for buoyancy-driven cavity like problem

Which turbulence model is suitable for resolving incompressible buoyancy-driven flow of a fluid within an cylindrical ampoule? I prefer turbulence model which is sufficiently simple so that fully ...
Jan Blechta's user avatar
9 votes
0 answers
448 views

What's a good numerical/optimization software package for solving the 2-D optimal stopping problem?

I am looking for a numerical software package to help me solve the 2-dimensional "free boundary" PDEs that arise in optimal stopping problems. In one dimension a standard optimal stopping problem in ...
Barney Hartman-Glaser's user avatar
9 votes
0 answers
163 views

Fast algorithms to solve Markov Decision Processes

In my master thesis I used an Algorithm called Approximative Dynamic Programming [1] to solve equations of the form $$ \max_{\pi}\mathbb{E}^{\pi}\left\{\sum_{t=0}^{T}\gamma^tC_t^{\pi}(S_t,A_t^{\pi}(...
Reza's user avatar
  • 191
8 votes
0 answers
293 views

Stable alternatives to "condition number"?

A number of numerical problems are easy to solve when condition number $\kappa$ of the problem is low. For instance, conjugate gradient descent complexity scales as $O(\sqrt{\kappa})$. However "...
Yaroslav Bulatov's user avatar
8 votes
0 answers
104 views

How do we approximate the numerical error a numerical scheme (e.g Runge Kutta, Euler etc) makes without having access to an analytical solution?

So I recently encountered this question in my head while taking my Scientific Computing class, where the lecturer talked about computing numerical error of a scheme. My guess would be that we take a ...
KARTIK BALI's user avatar
8 votes
0 answers
174 views

Is there a graphical interpretation or explanation of automatic differentiation compared to numerical differentiation

I have been looking at automatic differentiation for solving differential equations lately. I understand the basic ideas of using Dual numbers and such for finding derivatives, etc. However, I feel ...
krishnab's user avatar
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8 votes
0 answers
213 views

Why not use the preconditioned residual as termination criterion for preconditioned CG?

I have a Poisson equation with wildly varying material parameters (1 .. 1000), wildly varying element sizes (5 nm .. 100 um) and some quite anisotropic (tetrahedral) elements (100 nm x 100 um). I use (...
Thomas Klimpel's user avatar
8 votes
0 answers
111 views

How to construct an effective preconditioner for this particular problem

A quick introduction to my problem I am currently developing a method for simulation of water waves in three dimensions based on potential flow theory. The computational bottleneck of the method is ...
Mathias Klahn's user avatar
8 votes
0 answers
4k views

Good C++ optimization library for BFGS

To implement maximum likelihood estimators, I am looking for a good C++ optimization library that plays nicely with Eigen's matrix objects. Eigen has some capability of interfacing of its own but if ...
Hirek's user avatar
  • 183
8 votes
0 answers
136 views

Finding the smallest root of a function on $[0, \infty)$

I would like to find the smallest real root of a 1-D real-valued function $f(x)$ on the domain $x\in [0,\infty)$. In this problem, I can make the following guarantees on $f$: $f$ does have a root at ...
Endulum's user avatar
  • 735
8 votes
0 answers
580 views

Speed and accuracy of Strassen vs Winograd matrix multiplication algorithms

I am doing work which requires as fast matrix multiplication as possible and just want to double-check with this community that the Winograd variant of Strassen's MM algorithm is the fastest practical ...
kreitz's user avatar
  • 91
8 votes
0 answers
436 views

Eigenvalue with largest imaginary part

Iterative eigensolvers such as ARPACK, give the option to find a subset of the eigenvalues which have the largest imaginary part. My question is how do these algorithms work. As I understand it, ...
as2457's user avatar
  • 243
8 votes
0 answers
292 views

What can be done with Finite Element Method and not with the Finite Volume Method, and vice versa?

What are some applications where you would absolutely go for either FEM, but not FVM, or vice versa? What are some applications where both methods are equally suited? I worked with the FEM so far and ...
Michael's user avatar
  • 1,463
8 votes
0 answers
863 views

Numerical implementation of the Dirichlet-to-Neumann map

I am solving the Dirichlet problem $$ \begin{cases} \Delta u = 0, \\ u|_{\partial D} = f, \end{cases} $$ in a $2d$ domain $D$ using the finite element method. What I want to get is the ...
Appliqué's user avatar
  • 445
8 votes
0 answers
176 views

Tucker factorisation to compare multiple PCA decompositions?

This is an entry-level question for multiway matrix decompositions. I have a set/population $k$ of entities (here biological cells) for each of which I also have a number ($l$) of flavours of length $...
drw's user avatar
  • 203
8 votes
0 answers
577 views

DIIS method to accelerate SCF convergence for stretched geometries

I am implementing from scratch an Hartree-Fock calculation in the STO-3G basis set to perform Born-Oppenheimer molecular dynamics. I have a Restricted Hartree-Fock procedure that can reproduce very ...
user avatar
8 votes
0 answers
167 views

Accelerated convergence for Sparse NMF

In the Non-Negative Matrix factorization (NMF), you basically compute an approximation of a given matrix $V \in \mathbb{R}_{+}^{n \times m}$ into matrices $W$ and $H$ such that $W \in \mathbb{R}_{+}^{...
Gilles's user avatar
  • 253
8 votes
0 answers
789 views

What is the source of the error in the Sherman-Morrison formula application?

The Sherman-Morrison formula $$ (A+uv^T)^{-1} = A^{-1} - \frac{A^{-1}uv^TA^{-1}}{1+v^TA^{-1}u} $$ results in small errors in relation to the standard matrix inverse operation after each application, ...
rcpinto's user avatar
  • 180
8 votes
0 answers
148 views

Potential Reduction and Primal Path following methods

In both the potential reduction and primal path following interior point methods for linear programming, a barrier function is constructed which contains the terms $-\sum \log x_j$ where $x_j$ are the ...
Opt's user avatar
  • 341
8 votes
1 answer
137 views

Choosing how many iterations to use in VEGAS

I'm using VEGAS integration, specifically the GSL implementation, for some QCD calculations, and I've been investigating the behavior of the algorithm for various numbers of iterations in an attempt ...
David Z's user avatar
  • 3,383
7 votes
0 answers
276 views

Matrix-free FEM references

I've seen that many people are using matrix-free fem codes in my community (mechanical engineering). I have to admit that I googled a bit and I didn't manage to find a good reference for the subject. ...
FEGirl's user avatar
  • 311
7 votes
0 answers
86 views

Choice between using Moore-Penrose inverse and G2 inverse

Moore-Penrose inverse for an arbitrary matrix $X\in \mathbb{R}^{n \times p}$ is defined by a matrix $X^\dagger$ satisfying all of the Moore-Penrose conditions, namely \begin{align} (1) \;\;\;& XX^\...
waic's user avatar
  • 173
7 votes
0 answers
136 views

Can we sparse solve a few eigenvalues specified by index range?

I need to solve a few eigenvalues of a large sparse matrix specified by their index range. These indices are according to the whole eigenspectrum sorted in algebraic (not absolute value) ascending ...
xiaohuamao's user avatar
7 votes
0 answers
295 views

Finding points inside cells of power (generalized Voronoi) diagram

Suppose we have a set of points $p_1,\ldots,p_n\in\mathbb R^d$ as well as a set of weights $w_1,\ldots,w_n\in\mathbb R$. Recall that the power cell associated to the pair $(p_k,w_k)$ is given by: $$\...
Justin Solomon's user avatar
7 votes
0 answers
198 views

Is a complete bacteria simulation with an exascale supercomputer possible?

Will it be possible to simulate a complete (at least simple) bacteria atom by atom on an exascale supercomputer? or is it possible already today with the largest systems? Here, I've read that ...
Open Food Broker's user avatar
7 votes
0 answers
433 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 ...
Nico Schlömer's user avatar
7 votes
0 answers
578 views

How to check if my stiffness matrix is correct

I built the stiffness matrix for the Poisson equation on a 2-dimensional domain with the shape of "almost" an octagon, using pyramid basis functions. I used almost to intend the fact that I have an "...
slamWolfen's user avatar
7 votes
0 answers
170 views

"Geometry of ill-conditioning" for least-squares problems

It is an idea that dates back to Demmel, 1987 that the condition number of a problem is often related to the distance to the closest ill-posed problems. In Section 3 of the above paper, the author ...
Federico Poloni's user avatar
7 votes
0 answers
338 views

Implementation of Lanczos method that returns tridiagonal matrix

The Lanczos method can be used to obtain extremal eigenpairs of sparse symmetric or hermitian matrices. I know there are several implementations of the Lanczos method (as well as Arnoldi, Davidson, ...
delete000's user avatar
  • 171
7 votes
0 answers
573 views

Is there any catch on using `zgemm3m` vs regular `zgemm`?

I've just (to my embarrassment) encountered a BLAS-like extension of a matrix-matrix product subroutine gemm in Intel MKL: gemm3m...
Anton Menshov's user avatar
  • 8,662
7 votes
0 answers
96 views

Quadrature methods for peaky integrands

Consider $$ I = \int_{-L}^L f(x)dx, $$ where $f(x)$ is real-valued and analytic on $[-L,L]$, but it has a pole in the complex plane whose real part lies in $[-L,L]$. Call it $z_0$, and assume it is a ...
Endulum's user avatar
  • 735
7 votes
0 answers
223 views

Solving a coupled eigen value problem

I have the following problem: $$\begin{bmatrix}A &B \\C& D\end{bmatrix}\begin{bmatrix}x\\y\end{bmatrix} = \begin{bmatrix}\lambda I_m & 0 \\ 0& \mu I_n\end{bmatrix}\begin{bmatrix}x \\y\...
xadu's user avatar
  • 171
7 votes
0 answers
905 views

Sparse matrix format and sparse-matrix sparse-matrix multiplication

I'm having some performance problems with my code dealing with the multiplication of big sparse matrices (stiffness and aerodynamic influence coefficient matrices). Mainly I have to multiply such ...
murph_sof's user avatar
7 votes
0 answers
337 views

Compute sparsity pattern of $A^2$

Suppose we have a sparse matrix $A$. Is there any way to compute just the sparsity pattern of $A^2 = A \cdot A$ (I do not actually need to know what exactly the nonzero value are) faster than to ...
vainia's user avatar
  • 121
6 votes
0 answers
134 views

Runge-Kutta methods, higher derivative methods, and collocation methods

Consider an ODE system $$\dot x = f(t, x), \quad x(0) = \xi.$$ A collocation method to solve this ODE (1) assumes that $x$ can be approximated as a polynomial $x(t) \approx \sum_kx_kp_k(t)$ and (2) ...
Daniel Shapero's user avatar
6 votes
0 answers
118 views

References on the theory of Petrov-Galerkin methods for more "basic" problems

In my reading on various aspects of FEM, Petrov-Galerkin methods often arise in the study of solutions of convection-dominated systems, such as Hughes' work on Navier-Stokes, or systems where optimal ...
whpowell96's user avatar
  • 2,294
6 votes
0 answers
330 views

FEM : energy minimization VS PDE solving

Engineering FEM When I studied engineering, I learned the traditional approach for finite elements for elasticity. The point was to solve the PDE $-div(\sigma)=f$ as: Multiply your PDE with a test ...
Txnda's user avatar
  • 61
6 votes
0 answers
96 views

What is the best method to do a MC Integration of a multidimensional integral where the integration limits depend upon other variables?

What is the best method to do a Monte Carlo Integration of a multidimensional integral where the integration limits depend upon other variables? I am interested in getting a numerical value of a 5 ...
pollux33's user avatar

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