Questions tagged [scipy]
SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.
253
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Solving system of ODEs, where time derivative approaches infinity due top initial condition
I am trying to solve a problem in python using scipy's solve_ivp. The system of ODEs I am trying to solve is for coupled where I am solving for two time-dependent ...
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1
answer
79
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Weights for equidistant samples in power law fitting
I am working on fitting analytical curves to experimental data obtained in real viscoelastic tests (in fact, static creep tests).
The setting of the problem is:
the experimental data I have is a set ...
- 23
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answer
52
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2D integrals in Python with specified points of interest
Note: This is my first question on stackexchange; please tell me if I'm doing something incorrectly.
I am trying to calculate a series of a 2D integrals in Python with an integrand that has several ...
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67
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Using solve_ivp for a PDE: how to handle multiple time-dependent variables?
I am trying to build a Python code that solves a set of coupled differential equations which will be spatially discretized by the method of lines advancing in time. I am planning to use ...
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2
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170
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Solving IVP backward in time via python
I'm having difficulty solving an initial value problem (IVP) in Python backwards in time.
The code is at the end of this post.
First, please let me state my simplified problem.
The forward IVP is ...
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Matching the limits of integration with the proper variables in a complicated case when using scipy.integrate.nquad
I need to integrate expressions containing powers of the function:
...
6
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1
answer
148
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Accelerating the computation of scipy.sparse.linalg.expm_multiply
I have a tridiagonal antiHermitian matrix ($-i*Hami*t$) with nonzero elements only along the upper diagonal and lower diagonal, and the goal is to know the action of exponential of such matrix on a ...
- 63
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52
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Possible bug with scipy.optimize SHGO sobol: TypeError: <lambda>() takes 1 positional argument but 3 were given
I have been trying to perform some global optimization with SciPy optimizer SHGO
and I've had issues with the sampling method 'sobol'. Specifically, I get an error ...
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2
answers
88
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How do I evaluate the numerical solution at a point that isn't on the mesh
I'm trying to code a fixed-point method to solve the following system using scipy.integrate
$$
u_{n+1}(s)=\int_0^TK_\lambda(t,s)\left(\lambda u_n(t)+\sigma(t)+f(t, ...
- 35
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2
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42
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How to program the convergence of a sequence of systems of integral equations using Scipy
I'm trying to solve the problem
where $u_n$ and $v_n$ are sequences that converge to the solution $u$ and $v$ and $\lambda$, $\sigma$, $f$ and $g$ and K_lambda are all given.
I thought of using the ...
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Solving Transcendental equation involving special functions becoming nightmare any one can help?
Simply i want to solve for schrodinger equation for finite potential well problems in spherical coordinates. For case in which l=0 . It is simple but when l changes. The solution are spherical ...
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1
answer
100
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Need help to fully understand SciPy's odeint's reported step sizes, eval times, # of funct calls & total proc. time (re. question in Astronomy SE)
A recent question in Astronomy SE Numerical Programming using odeint takes more than 17 minutes got me interested in looking closer at SciPy's odeint.
The problem is a modified orbital mechanical ...
- 1,016
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86
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Scipy.root not converging even when provided with initial guesses very close to solution
I've made a previous question here and also in SO wondering why only the fsolve solver converges for the simple one dimensional unsteady conduction problem
$$ \frac{\partial T}{\partial t} = \alpha \...
- 133
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2
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257
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Why is this scipy.root code not converging?
I'm running a test problem to set up larger problems. Solving the simple unsteady heat equation via finite differences:
$$ \frac{\partial T}{\partial t} = \alpha \frac{\partial^2T}{\partial x^2}$$
$\...
- 133
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1
answer
134
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Solve 1st order ODE in using `scipy`
I've been trying to solve the following equation
$$
y(t)=-A\cdot\frac{\mathrm{d} y}{\mathrm{d} t}+B\cdot\left(\frac{\mathrm{d} y}{\mathrm{d} t}\right)^{2}+C
\\
y(t=0)=y_{0}\\
$$
where $A$, $B$, and $C$...
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2
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509
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Why does `scipy.optimize.minimize(...)` fail with this toy constrained minimisation case?
I'm learning scipy.optimize.minimize. I thought of a simple function to see how it works:
$$f(x) = x$$
With the goal to minimise $f(x)$, subject to the constraint ...
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1
vote
1
answer
88
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Solving basic barystochrone problem in python
I am trying to solve $\frac{u''}{1+u'^2} - \frac{1}{2(1-u)} = 0$ subject to $u(0)=1, u(1)=0$.
If I understand how to do this properly, I first do the variable substitutions:
$u = y$, $y_1 = y; y_2 = y'...
- 263
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0
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582
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ValueError: array must not contain infs or NaNs; When using solve_ivp in the scipy library
I am solving an initial value problem using solve_ivp. The problem consists of computing the concentration profile of a set of reactions over time, given the initial concentrations and some of the ...
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1
answer
116
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Interpolating 2D data on a hemisphere in order to have $C^2$ function but no overshoot
I am interpolating a 2D dataset on a hemisphere, and I am currently using scipy.Rbf that I like for its simplicity.
I am defining the norm of the interpolator with ...
- 63
1
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1
answer
404
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Beta function and integral value
I have two values $a$ and $b$ where $a \ge 0$ and $b \ge 0$ and I have to calculate the formula below.
$$
\frac{1}{2}\int_0^1\text{abs}\left[\left( \frac{p_i^{(a - 1)} \times (1 - p_i)^{(b - 1)}}{\...
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2
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875
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Fix step size with scipy.integrate.RK45 and scipy.integrate.LSODA
I am trying to numerically integrate a differential equation using scipy.integrate.RK45 and/or scipy.integrate.LSODA.
Now, I am trying to fix the integration step sizes of both solvers. This, however, ...
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votes
1
answer
93
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Scipy solve_ivp sensitivity to random phase shifts
I am trying to solve a coupled system of ODE's using the solve_ivp function from scipy. The general form of the equation is given via
$$\dot{y}(t) = M(t)y(t).$$
The time dependence of matrix is ...
- 31
3
votes
1
answer
537
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Using the Kramers-Kronig (Hilbert) transform in Python
I am trying to use the Kramers-Kronig algorithm to transform the real and imaginary contributions to the anomalous scattering factor from a diffraction anomalous fine structure (DAFS) experiment.
I ...
2
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1
answer
337
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How to extract intermediate calculation results from an SciPy ODE function in python?
I have a bit lengthier ODE function which was simulated by using Scipy solve_ivp function. During this simulation I calculated many parameters but as the output, I am taking out put only some other ...
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0
answers
94
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How to save multiplication computation time between a dense vector and a not that sparse matrix?
I am trying to compute $\mathbf{X}\mathbf{u}$ for many times in my algorithm, where $\mathbf{X}\in \mathbb{R}^{n\times m}$ and $\mathbf{u} \in \mathbb{R}^{m}$. The problem is that, during the ...
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1
answer
1k
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scipy.optimize.root not converging and RuntimeWarning
I am trying to solve the following problem:
$$ \frac{d^2y}{dx^2}=\sinh(y) $$
Where the boundary conditions are: $y(0)=-1$, and $ \frac{dy(x\rightarrow \infty)}{dx}=0 $. Through central difference ...
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1
answer
241
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Finding the parameters of a function via curve fit
I'm trying to estimate the parameters (v, n, k) defined in fit_func. I tried the default least squares fit but I couldn't find the parameters successfully.
...
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370
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Curve fitting using a piecewise polynomial
I am trying to fit a piecewise polynomial function
Code:
...
- 491
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1
answer
49
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Scipy QZ documentation
The scipy.linalg.qz function implements generalized Schur decomposition for a pair of matrices A, B such that
(A, B) = (Q @ AA @ Z*, Q @ BB @ Z*), where ...
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1
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771
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Fitting a monotonically increasing spline function
I want to fit a monotonically increasing smooth spline function for a dataset
Code:
...
- 491
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votes
2
answers
997
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Inaccurate results of integration using scipy solve_ivp
I am trying to use solve_ivp to solve the following 1st order ODE:
$$ \frac{d \rho}{d z} = \frac{m \theta}{(1+\theta z)} \, \rho, $$
subject to $\rho(z=0)=1$, where ...
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169
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SLSQP solver scipy with linear subset constraints
I have been trying to solve a least squares problem of the following form:
$$
\begin{equation}
\min_{\vec{x}} \frac{1}{2} \lVert f(\vec{x}) - f_{\text{target}} \rVert_{2}^2 + \alpha\Big( \frac{1-\rho}{...
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Using absolute error as the cost function
This is related to my previous post Minimize distance between curves.
I have a dataset with values of multiple curves. An example plot is shown below.
I want to scale the curves (move up/down) so that ...
- 491
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152
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Solving differential equations with fast oscillations using odeint
I have wrote this code to solve an equation , I know the behavior of this function has very rapid oscillations, when I RUN it gives bogus values for some "m[x]" and some "t"'s, ...
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1
vote
1
answer
261
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How to perform FFT from plane-wave basis function coefficients to real space?
I have a 3D grid in real space of grid spacing $L$ and say 21 grid points in each direction, containing e.g. a charge distribution. This is stored as a numpy array of shape ...
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-1
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1
answer
123
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Fitting gauss-hermite-parametrization to data?
I want to fit this data.
I have the following model functions. Classic gaussian:
def gauss_model(x, mu, sigma):
return np.exp(-0.5*((x-mu)/sigma)**2)
And ...
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1
vote
1
answer
357
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Huygens Fresnel Diffraction integral using dblquad in python
I am attempting to create a python function to assist in calculating the following numerical integration of the Huygens Fresnel integral in the form of ...
1
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0
answers
2k
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scipy.optimize.minimize fails to converge but result is OK
I am trying to optimize a non-linear least squares problem with scipy.optimize.minimize. I have simplified my actual problem down to the case where I am just computing the top 'principal components' ...
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1
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99
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Parameter estimation simple theory question related to scipy.optimize.curve_fit
It has been a while since I have done some stats, and I have tried to fit a curve using optimize.curve_fit of parameter estimation. I am also interested in the standard deviation of the fitted ...
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1
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1k
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Easy way to perform solver over pandas dataframe
I'm moving from Excel to Python and I'm trying to solve these equations:
$$\begin{align}
X_1&=\bigg[\big(3.47-\log(X_2)\big)^2+\big(\log(c)+1.22)^2\bigg]^{0.5}\\
X_2&=\frac{a}{101.32}\bigg(\...
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1
answer
313
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2nd order differential equation coupled to integro-differential equation in python
I'm trying to solve the following equations numerically in python
$$\begin{align}
12\pi\int_0^\infty drf(r)\phi(r)r^4&=E\\
f(r)-\frac{1}{2\mu}\bigg(\frac{d^2\phi(r)}{dr^2}+\frac{2}{r}\frac{d\phi(r)...
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1
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2k
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Optimal value of parameter/s from a set by scipy.optimize.minimize() method
I have this function $y = \exp(-x)$. I have a list of $x$ values and corresponding $y$ values.
...
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2
votes
1
answer
103
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Finding the correct order of eigenvectors of a parameter-dependent Hermitian matrix
so, I have a symmetric, analytic matrix $\mathbf{H}(x)$ ($x$ is real). Because $\mathbf{H}(x)$ is analytic and $x$ is real, it is possible to find analytic functions for the eigenvectors and the ...
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2
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1
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115
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SciPy ODR "Ordinary" Least Squares?
Scipy.odr has a setting for "fit types", including one for ordinary least-squares. This matches with the documentation of ODRPACK (see p. 31, Computational method).
However, the package ...
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1
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312
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Can't solve second order differential equation with scipy
Most of my knowledge about numerically solving differential equations is long forgotten. Unfortunately I stumbled upon a physics problem where I need to do exactly that.
I'm trying to describe the ...
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2
votes
1
answer
199
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Global convergence behavior of several Krylov solvers in scipy.opt
In the context of mechanical simulation, where I solve the stationary action principle directly (i.e. $\nabla S = 0$ for some scalar function $S$), I use the wrapper ...
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votes
1
answer
602
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How to solve a BVP with known parameters?
I need to solve a boundary value problem (BVP) of second order, where the equation depends on several know parameters, which are geometric parameters and material constants.
I would like to solve this ...
- 560
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0
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247
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Trouble inverting complex matrix with numpy and scipy
I have some matrix-valued, complex data $Z(f)$ with $f\in\{f_0,f_1,\dots\}$ and $Z(f_i)$ being a 3x3 matrix. I require the inverse $Z^{-1}(f)$ in my workflow. After encountering some problems with my ...
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106
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How to troubleshoot numerical instability using finite difference for steady-state non-linear heat conduction equation
I have a problem which I believe is numerical instability when trying to solve a heat conduction equation using finite difference. The short version is that when the parameter $I=80.3$ I get the blue ...
- 560
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1
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167
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