Questions tagged [scipy]
SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.
198
questions
0
votes
2answers
9 views
scipy odeint: excess work done on this call depending on initial values even with analytically solvable ODE
I am trying to solve a differential equation in the form:
dx/dt = funct(x)
using scipy odeint.
However, for some initial values, I get a "ODEintWarning: Excess work done on this call", even ...
-1
votes
0answers
34 views
Python approach for calculating a 2D matrix by interpolating 'between' two other 2D histograms [closed]
I have two 2D histograms, A and B, calculated from simulations by changing a single input parameter (alpha and beta set at "5" and "7", respectively). I want to calculate a third ...
1
vote
1answer
43 views
Efficiency of scipy.sparse.linalg.expm_multiply with sparse vs unsparse vectors
From the package scipy.sparse.linalg in Python, calling expm_multiply(X, v) allows you to compute the vector ...
-1
votes
0answers
19 views
Solve_ivp using timestep
I am trying to compute the path of a charged particle as it moves through a magnetic field. I am currently using a uniform field, but I am going to expand into nonuniform fields later on. The problem ...
-1
votes
1answer
99 views
Using ODE to plot particle-motion with scipy.integrate.solve_ivp
My Problem:
A positively charged particle (mass = 2 * 10-27 kg) is moving along the x-axis. It is travelling in a homogenous magnetic field such that the field axis in z-direction. The energy of the ...
-1
votes
1answer
77 views
Solving ODEs, Rotations, Angular Velocity, Euler Angles
I am implementing a simulation that needs to rotate and object based
on known angular velocity (assumed constant for simplicity). I followed the
ideas given below, pg. 32)
https://graphics.stanford....
-1
votes
1answer
77 views
Fitting using curve_fit of scipy in python gives totally different answer for 1/t and t
I was trying to fit some data to a single degree exponential decay function but a*exp(-x*t) and a*exp(-x/t) gives completely ...
-2
votes
2answers
86 views
numerical solution for differential equation
I have these 3 equations and i want to solve them with numerical methods. so I am using scipy library but I don't know how to solve 3 equations together.
R, g, sigma and density are constants.
\begin{...
1
vote
1answer
54 views
Eigenvalue problem for ordinary differential equation
I am trying to compute the natural frequency of a cantilevered beam.
The Euler-Bernoulli equation reduces to the following problem :
$$
v''''=\lambda v, \text{with }, v(0)=0, v'(0)=0, v'''(1)=0,v''(1)...
2
votes
3answers
159 views
Solving a PDE with 2 variables, with one variable whose derivative with respect to space is only known
I am trying to solve a PDE of the form
$$\frac{\partial u}{\partial t} = D \frac{\partial^2u}{\partial x^2} + k\ \ \ (1)$$
where only $k$'s first derivative with respect to $x$ is known
$$\frac{\...
3
votes
0answers
60 views
Does shift-invert method has invertibility issue?
Please note that I have nearly zero background on numerical methods.
I understand the shift invert method as described in SciPy Tutorial
The main argument of the above link is as follows. Suppose we ...
3
votes
0answers
57 views
Check if LinearOperator is symmetric
I have a scipy.sparse.linalg.LinearOperator object. I'd like to check if its associated matrix is symmetric without actually instantiating the matrix in the most ...
3
votes
1answer
95 views
Lanczos algorithm for finding top eigenvalues of a matrix sum
I am trying to find the top k leading eigenvalues of a NumPy matrix (using python dot product notation) L@L + a*X@X.T, where $L$ ...
0
votes
1answer
121 views
Error using scipy.integrate.solve_ivp: index error: the index 0 is out of bounds for axis 0 with size 0
I am recently working on the code based on the stick-slip phenomenon in Python. It's the stick-slip oscillator (chapter 3.4) in https://www.sciencedirect.com/science/article/pii/S0888327020301205.
And ...
-1
votes
1answer
72 views
illegal use of ODEINT
given the following system:
$$\frac{dP}{dt} = \alpha P(1-\frac{P}{K}) - \beta P I$$
$$\frac{dI}{dt} = \beta P I - \rho I$$
how do I solve the system numerically. as when I attempt to solve this is the ...
3
votes
0answers
50 views
Difference between wave vector and density matrix in numerical calculation of Schrödinger equation
I solved Schrödinger equation for a following tow-level time-dependent Hamiltonian numerically in two ways:
...
2
votes
0answers
66 views
Providing Jacobian as LinearOperator in scipy.optimize.root
I asked this question a few days ago on stackoverflow, but I figure scicomp.stackexchange is probably a better place. Sorry for the double post.
I want to solve a system of nonlinear equations using ...
0
votes
0answers
64 views
L2 norm optimization problem
I have an optimization problem where i need to find an image x, that is very close to x' such that:
monitor(x') is valid but monitor(x) is invalid. (output is valid
when the neural network output is ...
0
votes
2answers
69 views
bin 2d array such that each bin contains equal number of samples?
I'm trying to bin a 2d array of points such that each bin has an equal number of samples contained in it. This would mean having bins of differing ranges and possibly shapes.
I have seen this ...
3
votes
0answers
81 views
Python routine to calculate shape resonances of H2
I am currently doing a project in which my aim is to write a program that can be used to calculate single and multi-channel shape resonances. So I'm looking at bound states and quasi-bound states.
...
-1
votes
1answer
129 views
Integrate function with cumulative distibution function inside
I'm trying to integrate a function which is defined as func in my code below, a cumulative distribution function is inside:
...
-1
votes
1answer
89 views
Solve integral $ \int_{-\infty}^{\infty} e^{-x^2}dx$
i trying to solve this integral
$$\int_{-\infty}^{\infty} e^{-x^2}dx$$
I'm using this
CODE
...
1
vote
1answer
121 views
nquad Integration in SciPy
I am trying to self-learn SciPy and evaluate the following quadruple integral using scipy.integrate.nquad:
$$\int_{0}^{1} \int_{0}^{1} \int_{0}^{1} \int_{0}^{1-x} (...
-1
votes
1answer
438 views
ODEintWarning: Excess work done on this call (perhaps wrong Dfun type)
I was messing around with some numerical integration functions. I wrote an arbitrary differential equation to test my understanding, the code is as follows:
...
0
votes
1answer
174 views
How to compare 2D vector fields and minimize the difference?
I want to compare the field of two electrical currents and compare the resulting field to a magnetic dipol field and find magnetic momentum that minimizes the difference of the two fields.
My current ...
1
vote
1answer
291 views
Trouble with backwards time integration in Python
I am struggling with a rather basic numerical integration task: Using Python's scipy.integrate.solve_ivp module to integrate an ODE sytem backwards in time. As a test, I am using the following ODE ...
14
votes
3answers
5k views
How are scientific computing workflows faring on Apple's M1 hardware
The initial wave of reviews for Apple's M1 hardware are out, and there's lots of generic benchmarks and data on workflows on professional programs for creative users, but I haven't seen anyone talking ...
1
vote
1answer
114 views
Help with modified bessel functions
I'm trying to parse the following expression (Eq. 35 in The Magnetic Field in the Vicinity of Parallel and Twisted Three-Wire Cable Carrying Balanced Three-Phased Current) in Python and calculate its ...
3
votes
1answer
177 views
Good languages/packages for interior point optimization with non-linear constraints?
I'm currently using Python's scipy.optimize package to perform parameter estimation for a system of 10 ODEs. I have some observed data, and I'm trying to find the set of parameters which makes the ODE ...
0
votes
1answer
149 views
SciPy odeint fails in unpredictable ways on deterministic system of ODEs
I've been trying to solve the following (relatively simple) system of Lotka-Volterra ODEs in Python using SciPy's odeint:
$$\dot{z_1} = z_1 \left(- \sigma z_1 + \sigma z_2 + \rho z_3 - z_4 - z_5\right)...
1
vote
1answer
172 views
Is there a way to bound the values of a variable when using scipy.integrate.solve_ivp in python?
I want to solve an IVP in python with two variables, x and u, but I need the values of u to be between 0 and 1. Right now it is giving me a solution with negative values for u. Here is the code I have....
1
vote
1answer
536 views
scipy odeint: excess work done on this call and very sensitive to initial value
I am trying out odeint and received the error
'Excess work done on this call (perhaps wrong Dfun type).'.
The values returned are also super sensitive to small ...
1
vote
1answer
584 views
Numerical integration problem: IntegrationWarning The integral is probably divergent, or slowly convergent
I am trying to get the numerical integration of a function using scipy's integrate.quad as follows.
$$
\begin{equation}
G (\alpha) = \frac{4\alpha}{\pi}\int_0^{\...
2
votes
0answers
31 views
Scaling tensor approximation by symmetric tensor decomposition with SciPy's L-BFGS-B
I am trying to approximate a symmetric tensor of which the values are in the range of [1e-7,1e-4], by a symmetric tensor decomposition of lower rank. For this I am using the L-BFGS-B method in SciPy's ...
0
votes
1answer
93 views
Odeint error for nonlineal differential equations
I receive the following error when I run the code.
ODEintWarning: Excess work done on this call (perhaps wrong Dfun
type). Run with full_output = 1 to get quantitative information. warnings.warn(...
2
votes
2answers
426 views
Python scipy eigh(Arpack) giving wrong eigenvalues for generalized eigenvalue problem
I am trying to solve a generalized eigenvalue problem using Arpack, right now the code is using LAPACK but that's too slow, we only need a few eigenvalues and the matrices are sparse so using Arpack ...
3
votes
1answer
143 views
How to get a more accurate cancelation
I shall try to get to the point, so let me know if there is something left and you need more details.
I am solving a couple of equations that are not coupled explicitly, but their corresponding ...
1
vote
1answer
290 views
DOP853 integration method is missing (SciPy)
I was checking some integration methods provided by SciPy, in which the DOP853 should be included according to the webpage (https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate....
0
votes
0answers
28 views
Set of integrators do not consistently solve an equation in Python
I must solve the following second order differential equation:
$\delta \phi^{''}_{\mathbf{k}}+(3-\epsilon)\delta \phi^{'}_{\mathbf{k}}+\left(\frac{k^2}{a^2 H^2}+\frac{V_{,\phi\phi}}{H^2}-6\epsilon +4\...
0
votes
1answer
234 views
How to use cumtrapz correctly?
I have tried to do a trapeze integration with f(x)=x^2, where I know how the antiderivative looks like, so F(x) = (1/3)x^3
Here's my code, just like I tried:
...
2
votes
0answers
58 views
Non-negative Least Squares to perform Inverse Laplace with weights
I'm trying to perform the inverse Laplace transform of a (noisy) dataset $y_i$ using Tikhonov regularization:
$$\min \sum_{i=1}^{N} \left(\int_0^\infty e^{-s_i t} f(t) \, dt - y_i \right)^2 - \lambda^...
0
votes
0answers
113 views
scipy's solve_ivp returns erroneous results for a stiff differential equation
I'm using scipy's solve_ivp for solving a stiff differential equation. I'm using method BDF for solving the same.
I have already used MATLAB's ode23s and I'm getting correct results in MATLAB.
However,...
0
votes
0answers
135 views
A parallelized GMRES solver?
My application calls for solving a dense, 40,000 x 40,000, ill-conditioned linear system. The native SciPy GMRES solver with preconditioning has worked well for my application and solving a single ...
6
votes
3answers
323 views
Is LAPACK behind the cutting edge of dense linear algebra?
I have been digging into some numerical linear algebra lately, and reading in particular about how LAPACK solves symmetric eigenvalue problems. I noticed that the ...
0
votes
0answers
32 views
Comparing custom linear regression solver to SciPy equivalent in Python
From a given data set, I set out to complete a task which is below
Fit the data of the previous exercise to fit Eq. (8.18) using the SciPy function ...
2
votes
1answer
79 views
Functions from Scipy, Blas, or Lapack that compute only upper triangular matrix
My goal is to transform a matrix into upper triangular form in Python. I know the function scipy.linalg.lu will do LU decomposition and get both upper and lower ...
3
votes
1answer
388 views
Why is 'scipy.sparse.linalg.spilu' less efficient than 'scipy.linalg.lu' for sparse matrix?
I have a matrix B which is sparse and try to utilize a function scipy.sparse.linalg.spilu specialized for sparse matrix to ...
5
votes
1answer
164 views
Algorithm to factorize matrix whose many rows are already of upper triangular form?
I have a matrix whose many rows are already in the upper triangular form.
$$\begin{bmatrix}
x_{11} & x_{12} & x_{13} & x_{14} & x_{5} \\
0 & x_{22} & x_{23} & x_{...
3
votes
2answers
674 views
Computing numeric derivative via FFT - SciPy
I wrote the following code to compute the approximate derivative of a function using FFT:
...
3
votes
1answer
241 views
Fast nonzero indices per row/column for (sparse) 2D numpy array
I am looking for the fastest way to obtain a list of the nonzero indices of a 2D array per row and per column. The following is a working piece of code:
...
