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4
votes
1answer
291 views

Nelder-Mead optimization Algorithm

I am reading the following file, that explain the Nelder-Mead optimization Algorithm.(Algorithm Below) Where $B$ is the best point, $G$ second best point, $W$ is the worst point, $R$ reflection point. ...
14
votes
5answers
560 views

Examples of PDE computations using parallelism in both space and time

In the numerical solution of initial boundary value PDEs, it is very common to employ parallelism in space. It is much less common to employ some form of parallelism in the time discretization, and ...
6
votes
2answers
6k views

Recommendations for a usable, fast Java matrix library?

This complements an earlier question on usable, fast C++ matrix libraries. I've looked at the Java Matrix Benchmark, and it seems like the performance of java matrix libraries is all over the place. ...
5
votes
2answers
1k views

Monte Carlo simulation of 3D X-Y model

I need to compute the helicity modulus as a function of temperature for a three-dimensional X-Y model (see N.K. Kultanov, Yu.E. Lozovik, "The critical behavior of the 3D X-Y model and its relation ...
3
votes
2answers
3k views

How to let OpenFOAM abort a simulation when values exceed a given range?

When the absolute pressure becomes negative or $U$ exceeds the speed of light, things have pretty obviously gone wrong (be that bad boundary conditions, a too coarse mesh, a too large timestep etc.). ...
7
votes
1answer
684 views

C library - iterative sparse complex linear equation solver?

Where can I find a library to solve a sparse complex matrix equation iteratively in C. So far I've only found libraries for direct solution to complex systems, and libraries for iterative solutions to ...
12
votes
4answers
5k views

Efficient interpolation method for unstructured grids?

I would like to know a good method for interpolating data between two unstructured grids, where one grid is a coarser version of the other. Efficiency is very important to me since I'm solving a ...
13
votes
5answers
4k views

How can I approximate an improper integral?

I have a function $f(x,y,z)$ such that $\int_{R^3} f(x,y,z)dV$ is finite, and I want to approximate this integral. I'm familiar with quadrature rules and monte carlo approximations of integrals, ...
0
votes
0answers
88 views

Produce equation of curve, given some coordinates [duplicate]

Possible Duplicate: Get equation for a curve which intersects x at seemingly randomly distributed points? I tried asking something similar to this before, but I guess I didn't explain very well. ...
11
votes
3answers
1k views

Libraries for solving Lyapunov's equation

The following matrix equation $$B\Sigma + \Sigma B^T + C = 0$$ in $\Sigma$ $-$ for given $B$ and $C$ matrices $-$ appears in my work as a characterization of a covariance matrix. I have learned that ...
16
votes
3answers
5k views

Finding which triangles points are in

Suppose I have a 2D mesh consisting of nonoverlapping triangles $\{T_k\}_{k=1}^N$, and a set of points $\{p_i\}_{i=1}^M \subset \cup_{k=1}^N T_K$. What is the best way to determine which triangle each ...
3
votes
1answer
108 views

Numerically stable real solution(s) to a system of bivariate quadratics

I have a a system of bivariate polynomials as follows: $ E(u,v): e_2(u) v^2 + e_1(u) v + e_0(v) = 0 \\ F(u,v): f_2(u) v^2 + f_1(u) v + f_0(v) = 0$ where $e_n(u) = e_{n_2}u^2 + e_{n_1} u + e_{n_0}$ ...
4
votes
2answers
3k views

What is the most efficient way to diagonalize small matrices?

I have a problem where I need to diagonalize a large number of small Hermitian matrices. Typically the matrices are between 4 and 64 in size (skewed towards the low end) and the number of matrices is ...
2
votes
0answers
618 views

Finding a permutation that makes a matrix lower triangular

I have a system of linear equations in form of $AX=b$ where $A_{m\times n}$, $X_{n\times 1}$ and $b_{m\times 1}$. Coefficient matrix $A$ is quite sparse. However, using a practical LP solver like ...
4
votes
2answers
1k views

LP feasibility checking

I have a linear programming problem. I want to know if this LP is feasible. What is the best known algorithm for checking feasibility of an LP or a linear system of equations?
4
votes
3answers
983 views

Applications of Moore - Penrose generalized inverse of a matrix and associated projection?

I am seeking applications in the industry for the Moore-Penrose generalized inverse $A^\dagger$ of a matrix $A$. The Moore-Penrose Inverse of $A\in \mathbb{C}^{m\times n}$, denoted by $A^\dagger$, ...
9
votes
1answer
2k views

How to find Lyapunov exponent for coupled system

Answer gives a software for calculating conditional Lyapunov exponent (CLE) for coupled oscillators in chaos synchronization. However, it is hard to follow and there is no graphical output of the ...
1
vote
1answer
204 views

Why isn't every linear program combinatorial?

A linear program (LP) \begin{alignat}{1} & \min_{x} {c}^{T}x, \\ \mathrm{s.t.} & \quad Ax = b, \\ & x \geq 0. \end{alignat} is called combinatorial if the size of entries of matrix $A \...
1
vote
0answers
84 views

Proportional equality constraints

Consider a node $s$. Let's assume that there are three outgoing arcs from node $s$ namely $(s,i)$,$(s,j)$ and $(s,k)$. Corresponding to each of these arcs, there is a flow proportion value $t_{sj}\in (...
2
votes
2answers
520 views

Exploring feasible points in a linearly defined space

What is the quickest way to find a point inside a linear feasible space? (Defined by the intersection of several hyperplanes and halfspaces). I want to be able to choose an initial point in the ...
13
votes
3answers
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 ...
5
votes
2answers
236 views

CFD for high-detailed turbulence and non-linear waves

What are typical (or promising) techniques and methods in CFD to achieve high-detailed turbulence and non-linear waves interaction? And with "active" geometry (when bodies interacts with fluid in both ...
8
votes
1answer
1k views

What are the strategies for local Adaptive Mesh Refinement (local AMR) on unstructured meshes?

I am interested in local AMR on unstructured meshes. Currently, I'm working with the OpenFOAM library - it supports completely unstructured local AMR: cell refinement criteria determine a list of ...
14
votes
6answers
1k views

Approximate spectrum of a large matrix

I want to compute the spectrum (all the eigenvalues) of a large sparse matrix (hundreds of thousands of rows). This is hard. I am willing to settle for an approximation. Are there approximation ...
5
votes
1answer
2k views

eigenvalues (and determinant) of a hadamard product of matrices

I need to compute the determinant of a matrix that is calculated as $B \circ A$, with $B$ and $A$ being square matrices and $\circ$ representing their Hadamard product. One way of doing this is ...
13
votes
3answers
1k views

SVD for finding the largest eigenvalue of a 50x50 matrix — am I wasting significant amounts of time?

I've got a program that computes the largest eigenvalue of many real symmetric 50x50 matrices by performing singular-value decompositions on all of them. The SVD is a bottleneck in the program. Are ...
2
votes
1answer
1k views

f2py: error f90 not supported by GnuFCompiler needed for source_file.f90

I'm trying to install a Python package that relies on extensions built from Fortran 90 using f2py, but I get the following error: ...
3
votes
2answers
311 views

Computing Permanents of $64 \times 64$ Matrices

I need to compute the Matrix Permanents of several $64 \times 64$, zero-one matrices. I have tried using the built in functions in both Sage and Maple, but both programs return out of memory errors. I ...
7
votes
5answers
594 views

What algorithm for solving a set of stiff ODEs would be easiest to port to high precision floating point arithmetic?

I want to solve a relatively small system of stiff ODEs (< 10 first-order equations) using high precision floating point arithmetic (using MPFR or alike). What would be the easiest algorithm to ...
16
votes
1answer
3k views

Drawbacks of Newton-Raphson approximation with approximate numerical derivative

Suppose I have some function $f$ and I want to find $x$ such that $f(x)\approx 0$. I might use the Newton-Raphson method. But this requires that I know the derivative function $f'(x)$. An analytic ...
6
votes
3answers
277 views

efficiently solving a low rank linear parametric systems?

I have a large number of systems of the form: $Ax=b_i$ To solve for a large numbers of such $b_i\;1\leq i \leq k$ but where $A$ is fixed (A is a rank $p$ general --i.e. non sparse, non PSD-- ...
3
votes
1answer
216 views

Different kinds of Integral Equation Methods

I am relatively new to integral equations for solving time-harmonic EM scattering problems. I have read a decent number of papers on the subject, and it seems that for formulations that can support 3D ...
3
votes
2answers
386 views

Get equation for a curve which intersects x at seemingly randomly distributed points?

Is there any type of function that when graphed would show a curve which intersects the x axis multiple times, with each point being an arbitrary distance from the last? I mean, not like a trig ...
7
votes
5answers
9k views

Interpolate 2D data

I generated a cartesian grid in Python using NumPy's linspace and meshgrid, and I obtained some data over this 2D grid from an ...
8
votes
4answers
8k views

Is there an in practice limit on the number of constraints on a linear programming problem?

I am new to linear programming and have formulated a linear program (LP) with order of $10^{13}$ variables and $10^{13}$ constraints, although the constraint matrix is extremely sparse. I wanted to ...
15
votes
1answer
1k views

How to numerically calculate residues?

I need to calculate the following integral: $$ {1\over 2\pi i} \int_C f(E) \, d E $$ $$ f(E) = {\rm Tr}\,\left(({\bf h} + E)\,{\bf G}(E) \right) $$ Where $\bf h$ is a matrix (one particle kinetic and ...
7
votes
3answers
807 views

How to handle large numbers of output data sets from a simulation/sensitivity analysis?

Somewhat related, but I think the question is distinct enough to justify a separate question. As a bit of background, I come from a observational/statistical Epidemiology background, working with ...
34
votes
8answers
891 views

How do I make sure that the results of my simulations and the results in my paper are always in sync?

In one of my papers, I list some numerical results in addition to some figures. What I'd like to do is make sure that the numerical results in my paper always agree with the code. Right now, I just ...
5
votes
2answers
4k views

Specifying boundary conditions for imported mesh in OpenFOAM

I have a mesh produced from scanning a real 3D object (I don't have a geometry). What is the most convenient way to specify inlets, outlets, etc. for CFD in OpenFOAM? The mesh consists of thousands of ...
9
votes
3answers
3k views

How do I know if my code is being vectorized by the compiler?

As exemplified by Jed Brown's answer to Costs of lookups versus calculations, using vectorized vs non-vectorized floating point operations results in much faster code. Many modern compilers claim ...
3
votes
1answer
823 views

Where can I find coded examples of stochastic collocation applied to an elliptical PDE using smolyak sampling?

I'm having some troubles implementing a collocation method to solve a stochastic partial differential equation of the form: $\nabla (a(x,w)\nabla u(x,w))=f(x,w)$ in $D$, $u=g$ in $\partial D$ where $...
2
votes
1answer
77 views

Computing a sequence of row interchanges that realizes a given permutation matrix?

This question is aimed at cleaning up an implementation detail of an in-house sparse direct solver. It uses METIS to reorder $A$ into $PAP^{T}$ for reduced fill-in. Inside the $Lx=b$ and $L^{T}x=b$ ...
17
votes
2answers
8k views

Null-space of a rectangular dense matrix

Given a dense matrix $$A \in R^{m \times n}, m >> n; max(m) \approx 100000 $$ what is the best way to find its null-space basis within some tolerance $\epsilon$? Based on that basis can I then ...
4
votes
1answer
292 views

Should I include integral constraints in a integer linear program with a totally unimodular constaint matrix?

I have formulated an integer linear program (ILP). The constraint matrix for the ILP is totally unimodular. Should I solve it as an LP without the integral constraints, or should I keep the integral ...
3
votes
2answers
924 views

How to detect key turning points on a driven road?

I am looking for a description of algorithm which allows me to detect key turning points on the road amongs a set of all given points. I've ilustrated my problem on the below image: Green spots: ...
4
votes
1answer
256 views

Defining electric current source excitations for surface integral equation formulations

In a finite difference (FD) based electromagnetic formulation based on a Yee cell grid, one can define electric current source excitations ($J$) on the $E$ field grid points. At a distance, the fields ...
9
votes
2answers
178 views

Predict runtimes for dense linear algebra

I would like to predict runtimes for dense linear algebra operations on a specific architecture using a specific library. I would like to learn a model that approximates the function $F_{op} \;::\; $...
3
votes
1answer
607 views

Quality open source AMR libraries [duplicate]

Possible Duplicate: Is there a general-purpose library for structured grid adaptive mesh refinement? I'm looking for a quality, open source, maintained, scalable automated mesh refinement library ...
31
votes
4answers
2k views

What tools or approaches are available to speed up code written in Python?

Background: I think I might want to port some code that calculates matrix exponential-vector products using a Krylov subspace method from MATLAB to Python. (Specifically, Jitse Niesen's expmvp ...
4
votes
2answers
1k views

Line search for Newton method

If we want to solve nonlinear minimization problem $$\min_{x} f(x),$$ making least-squares assumption and using Gauss-Newton method so that at k$th$ iteration we have: $$J_k^T J_k p_k = - J_k^T ...

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