Questions tagged [jacobian]

Questions related to the calculation or use of the Jacobian matrix or its determinant. Not to be confused with the Jacobi iterative method for solving systems of linear equations. For those, use [iterative-method] instead.

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70 views

Method of Lines: How to simplify Jacobian with periodic BCs?

Consider the advection equation $$\frac{\partial u}{\partial t}+c(x)\frac{\partial u}{\partial x}=0.$$ With periodic boundary condtitions in $x$ with period $L$, i.e. $u(x,t)=u(x+L,t)$ and initial ...
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2answers
282 views

How to determine the Jacobian Ratio for triangle element?

I am trying to implement an algorithm to find the Jacobian ratio for each triangle in mesh as a part of mesh quality check. Let's say that I have vertices of the triangle: $P_1(x_1, y_1, z_1)$, $P_2(...
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1answer
51 views

Does the k-th approximate solution of a stationary iteration belong to the k-th Krylov subspace?

For an stationary iteration method solving $Ax=b$ as follows: $$ Mx_k = Nx_{k-1}+b, $$ I have known that when $M = I$, i.e., the Richardson iteration, the k-th solution $x_k = x_{k-1}+r_{k-1}$ is in ...
3
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1answer
95 views

Calculating the jacobian of norm and square root terms in the Finite Element Method

In the code that my group is writing (Lethe) we use a stabilized approach to solve the Navier-Stokes equation. The GLS stabilized method we use has a stabilisation term which contains a stabilization ...
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0answers
116 views

Jacobian-free approach for time-dependent equations for implicit time-stepping

When solving time-dependent non-linear equations, such as the non-linear diffusion equation $$\partial_tu=\nabla\left(D(u)\nabla u\right)$$ usually Newton's method is applied, with (coupled with the ...
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0answers
28 views

On using Ritz Method to solve a Mindlin–Reissner plate

I am trying to replicate the method given in the this paper. I have written a Matlab program which determines the displacement field of Mindlin–Reissner plate theory using Ritz method. The limitation ...
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0answers
76 views

Numerically Approximating the Jacobian and Comparing the Eigenvalues With Analytical Form

I am trying to study the stability of numerical discretization schemes using the Jacobian matrix of the residues with respect to the vector of conserved variables. For a simple diffusion equation ...
0
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1answer
75 views

Numerical Stability of a Generalized Spatial Discretization Scheme

After reading the matrix stability chapter (10) of Hirsch [1], I decided to dive in the reference list of the chapter. One of the papers [2], which is cited as reference shows an very interesting ...
3
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0answers
32 views

Detecting blocks in non-linear system of equations

When solving systems of non-linear equations using Newton's method, it is often observed that the system has an independent sub-system, e.g. : $$ f(x,y) = 0 $$ $$ g(x,y) = 0 $$ $$ h(x,y,z) = 0 $$ If ...
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1answer
71 views

Debugging Newton-method used in a CG-approach

I am currently proof-checking my program, which is intended to use Newton's method for solving nonlinear equations, using a continuous galerkin approach. Thus, as first step I checked it using a time-...
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2answers
268 views

Implementation of the Jacobian-free Newton method

In my calculation (of a simple heat equation, for testing) using the Newton method, I tried to replace the full Jacobian matrix with an approximation vector, i.e. replacing $J$ in $$J(u)\delta u=-F(u)...
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1answer
167 views

Shooting method implementation

I have a trouble of defining a Jacobian matrix for my problem. Basically, I have 4 differential equations to be solved. $$ \begin{aligned} \dot x_1(t)&=x_2(t)\\ \dot x_2(t)&=p_2(t)−\sqrt 2 ...
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1answer
388 views

What is the fastest method to invert millions of matrices?

My project involves large simulation and estimation. For each simulation I need to solve 600,000 systems of nonlinear equations. Currently I am using Newton's method to find the solutions. That ...
7
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2answers
362 views

How to calculate/derive analytic FEM Newton Jacobian

I trying to wrap my head of derivation of the analytic FEM Jacobian for the Newton method. Say we have a nonlinear Poisson problem of the (weak) form $$ \int a(u)\nabla\ u\cdot \nabla v = \int f v $$ ...
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1answer
147 views

How to verify solution to pre-conditioned linear systems solver?

I am solving Ax=b. A has a very large condition number (> O(10^10)) I am using the conjugate gradients method with point jacobi pre-conditioning. I obtained a solution 'x' that "looks" reasonable. ...
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0answers
500 views

Newton - Raphson method : maxima of function in 2 variables

I am computing the maximum of a function (with two-variables) using Newton-Raphson method. The function is : $e^{-(x \ - x_0)^2 - (y \ - y_0)^2}$, whose maxima exists at $(x_0,y_0)$. The Jacobian ...
1
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1answer
634 views

Confusion about determining the jacobian in a rootfinding algorithm

I have written some Python code to determine the numerical roots of the following non-linear equation: $$f_m=\tan\lambda_m - \frac{\lambda_m}{1+a}$$ where $\lambda_m\gt0$ and $a\geq0$. The code is: <...
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1answer
396 views

FEM on tet10 element: negetive determinant at the Gauss point

I am trying to implement a fem code on tet10 elements. I follow the lecture notes for tet10 implementation given in http://www.colorado.edu/engineering/CAS/courses.d/AFEM.d/AFEM.Ch10.d/AFEM.Ch10.pdf ...
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0answers
62 views

FEM/FVM/FD for structural modeling and stability issues due to large structural constants?

I've read that in modeling structures problems, the finite element method (FEM) is typically used. I am unfamiliar with FEM, but I am wondering, in particular, if using FEM, as opposed to finite ...
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1answer
2k views

How Jacobian matrix helps optimization faster?

I tried some python optimization functions and some of them needed Jacobian matrix prior for faster convergence. I understand Jacobians are basically transformation matrices that data from one space ...
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2answers
343 views

Sanity checking jacobians for Finite Element code

I have a legacy DG finite element code for which I would like to write some unit tests. As it is written, for 2D problems, each degree of freedom has associated with it a Jacobian matrix (for later ...
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1answer
7k views

Implementation of the Jacobi iteration to find the solution to $Ax = b$

I implemented the Jacobi iteration using Matlab based on this paper, and the code is as follows: ...
2
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1answer
5k views

Calculate Jacobian of triangular element given coordinates of vertices and displacements?

I am trying to determine quality of my mesh elements using the Jacobian determinant as the measure. My algorithm takes vertices of nodes in triangular mesh and moves them around so as to form ...
2
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0answers
52 views

Optimal ordering in Jacobi SVD algorithm

In Jacobi SVD algorithm as given here every pair of columns of the matrix is orthogonalized until convergence. I want to know that how does the order of selection of the pair of columns affect the ...
4
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1answer
168 views

Does the limit of $\frac{\partial f}{\partial u}$ at $u=0$ exist?

For an optimization routine I needed to compute the derivative of the right-hand side $\: f_u(x_k, u_k)$ of a discrete-time system $x_{k+1} = f(x_k, u_k)$. Since $\: f_u(x_k, u_k)$ includes terms that ...
4
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1answer
2k views

Newton's method goes to zero determinant Jacobian

I am using the Newton's method to solve $3\times3$ systems. For some particular cases, it turns out that at a given iteration, the Jacobian matrix cannot be inverted and that its determinant is very ...
2
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2answers
275 views

Ill-conditioned Jacobian matrix from Nernst-Planck equation with Butler-Volmer reactions

The governing equations are listed here of my notes on page 4. It's a reproduction of other's paper which solves the equations with COMSOL. The problems arise when I want to solve for the consistent ...
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0answers
61 views

“Damping factor” for a set of non-linear ODEs

I have a set of four non-linear ODEs representing a negative feedback. I have done parameter variation by random sampling to study the sensitivity of steady state and other dynamic properties to ...
2
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0answers
132 views

Rank deficient Jacobian in discretized periodic solutions to autonomous ODE

I'm trying to numerically find periodic solutions to different systems of autonomous nonlinear ordinary differential equations. I decided to use a finite difference scheme and solve the resulting ...
2
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0answers
571 views

Jacobian-Free Newton-Krylov vs explicitly forming jacobian in DG

For a given discontinuous galerkin (DG) implementation for Navier-Stokes, targeting 10,000 to 1,000,000 4th order cells in 3D, I'm using PETSc's suite of linear/non-linear solvers on the back-end. It ...
2
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1answer
671 views

Is there a relatively simple way to extract the Jacobian from a Runge-Kutta 4/5 integrator?

I have a RKF45 numerical integrator that simulates polymerization of proteins using CUDA. It does so by tracking the populations of discrete length polymers, e.g. monomers, dimers, trimers, etc. all ...
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2answers
1k views

Levenberg-marquardt: How to calculate the jacobian with fixed parameters

So I'm working on a fitting algorithm using the levenberg-marquardt algorithm and I'm a bit stumped as to how to handle fixed parameters. Looking around at other code, like the minpack version of the ...
4
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2answers
164 views

Non-linear root finding with positive definite Jacobian

I am dealing with a system of non-linear equations: $$ f(\boldsymbol{x}) = \boldsymbol{y}, \;\;\; \boldsymbol{x}, \boldsymbol{y} \in \mathbb{R}^d. $$ And I know that the Jacobian $J(\boldsymbol{x})$ ...
4
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2answers
486 views

Poisson-Nernst-Planck equations with ill-conditioned sparse matrix

I am trying to solve Poisson-Nernst-Planck system of equations for ions diffusion problem using finite volume method. Nernst-Planck equation for mass transport and Poisson equation for electrostatic ...
2
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1answer
383 views

How Matlab optimization works without Jacobian or Hessian

How does Matlab optimization tools works? It just gets the error function and doesn't need Jacobian (first derivatives) or Hessian (second derivatives)? How it is possible? If it is finite difference ...
10
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5answers
431 views

How to deal with complexity in numerical code, for example, when dealing with large Jacobian matrices?

I am solving a non-linear system of coupled equations, and have calculated the Jacobian of the discretised system. The result is really complicated, below are (only!) the first 3 columns of a $3\times ...