Questions tagged [computational-physics]

Computational physics is the study and implementation of numerical algorithms to solve problems in physics for which a quantitative theory already exists.

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Why this LJ molecular dynamics result doesn't converge?

I am doing a molecular dynamics simulation of Leonard Jones 6-12 potential.But instead of converging to a particular value. It always stays between -5.2 to -5.35. The standard value is -5.517. The ...
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8 views

How long should the hyperelastic equations be solved before updating the mesh?

How long should the hyperelastic equations be solved before updating the mesh? To be specific, I'm interested in the hyperelastic model with a neo-Hookean solid: $$ \nabla\cdot\sigma + f = \rho\ddot{...
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1answer
27 views

Numpys `tensordot` and what is happening mathematically

I've encountered a program where np.tensordot was used, so I tried looking it up but I can't really understand what this function is doing... I feel rather ...
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1answer
37 views

Is this behaviour normal for a Leonard Jones monte carlo simulation?

I am simulating a Leonard Jones fluid using MC simulation. The code always uses a reduced unit. I want to find the potential energy of the system.Periodic boundary condition implemented . I have ...
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1answer
32 views

How to get free energy surface of a 3d Ising Spin system using Monte Carlo simulation?

I am doing a Monte Carlo Simulation of the properties of a 3D Ising Spin system. I want to get the free energy surface of the spin system from the simulation. It is a magnetization vs free energy ...
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1answer
55 views

Why the magnetisation shows abrupt behaviour for this 3D ising spin system

I am trying to simulate a 3D Ising spin system (+1 & -1) using Monte Carlo Metropolis Algorithm. I want to get different physical quantities from this simulation like magnetization, Average Energy,...
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20 views

How can I compute electronic coupling 'H' for estimating the standard rate k_o from Marcus-Hush-Chidsey theory during heterogenous electron transfer?

I am trying to calculate the Marcus-Hush rate constant k_o for heterogeneous electron transfer in the context of a monolayer redox couple as described in Eq. (11) in this paper [ doi:10.1016/j....
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28 views

Why does torque kill my Job? [closed]

I am using PBS Torque scheduler to run my replica exchange molecular dynamics jobs. I am using Sander.MPI of AMBER to run some DFTB simulations. The problem I am having is that my jobs keep crashing ...
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1answer
112 views

Absence of Discontinuity in Specific Heat Plot Simulated by Ising Model

I am working on 2D Ising model, when I plot "specific heat vs temperature", I can't see any discontinuity at critical temperature around Tc ~ 2.7K. I am enclosing results of all other thermodynamic ...
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33 views

Unconditionally stable numerical method for 1st order non-linear coupled ODEs?

I am attempting to numerically solve the following system of ODEs: $$\begin{gather}\frac{dT_1}{dt} = f_1(T_1,T_2), \quad T_1(t=0)=T_{1,0} \\[3pt] \frac{dT_2}{dt} = f_2(T_1,T_2), \quad T_2(t=0)=T_{2,0}...
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31 views

Verification of Code

I am currently stuck with implementing some code. I need to plot L^2 against ∆t but I am not sure how to write L^2 as code, I have the numerical and exact solutions in my code and I am currently ...
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3answers
128 views

What numerical methods are used to model deformations in elastic physics?

What numerical methods are used to model deformations in elastic physics? For example, here's an example of a hyperelastic deformation in Ansys: Perhaps more simply than hyperelasticity, for linear ...
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1answer
70 views

Using Implicit Euler with second order differential equations

We can numerically integrate first order differential equations using Euler method like this: $$y_{n+1} = y_n + hf(t_n, y_n)$$ And with Implicit Euler like this: $$y_{n+1} = y_n + hf(t_{n+1},y _{n+...
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1answer
85 views

If not MATLAB, what software/programming language should I use to simulate/animate wave functions in various potentials + more? (example given)

I want to integrate programming into my learning in math and science in a very specific way. I want to create visualizations and simulations of concepts I am learning. When I learn a numerical method ...
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2answers
67 views

What is an instance (precisely) in computational complexity?

I am trying to understand the notion of reduction of a problem to another problem. As it is known this has huge impact on classifying the complexity of a problem. The definition of reduction involves ...
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0answers
31 views

Information resources on the discrete element method (DEM)

A am looking for online resources, which deal with topics related to DEM. I have been heavily involved with computation fluid dynamics (CFD) so far, and I am relatively new to the field of DEM. In ...
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76 views

Parallel plate capacitor as simple superposition of Coulomb-fields

I am trying to calculate and visualize the electric field inside and outside of a parallel plate capacitor by assuming a uniform distribution of point charges on each plate and by adding up the ...
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1answer
76 views

Operator splitting to solve time dependent Schrödinger equation

I encountered the split operator method to solve the time dependent Schrödinger equation during a lecture. I understand the method on a theoretical basis (I think at least), but I'm struggling to ...
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1answer
80 views

Fourier spectral method for coordinate transformed heat equation

As the title said, I want to solve a coordinate transformed heat equation using fourier spectral method. In particular, I am interested in transforming an uniform grid into an adaptive non-uniform ...
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1answer
69 views

Numerical integration methods: Explicit vs Semi-Implicit vs Newton-Euler 1, 2 and use in cyclone physics engine

I am trying to understand the difference between explicit Euler and semi-implicit Euler integration, where in explicit Euler the current position is calculated as $$x_{n+1} = x_n + v_n$$ and semi-...
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1answer
70 views

What is the relationship between shape functions, interpolation functions, and degrees of freedom?

I am a newbie in FEM. I would like to get clarity regarding a few questions on shape functions in this post (please use as simple language as possible). What is the relation between Shape function ...
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0answers
39 views

Propagation of a Gaussian beam using FFT

I am trying to simulate the propagation of a gaussian beam through a lens using an FFT approach. I tried to implement the approach described by Couairon in this paper at page 43: https://link....
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2answers
204 views

How to simulate over 1 billion particles?

I want to simulate human erythrocytes in capillaries. I calculated, that for a 1 meter long and 1 mm in diameter capillary there are about 3 billion blood cells. Erythrocytes are actually discs, but ...
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0answers
53 views

Is it possble to do this complex symbolic calculation with Matlab?

Sorry it's bit abrupt, but recently I am caught up in some symbolic calcualtion which is tedious and almost impossible with mere human hands, so just wondering is it possible to solve the double ...
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1answer
106 views

Calculation of Mean Square Displacement for Brownian dynamics system with Lennard Jones interactions in python3

I have a problem getting a sensible result for the Mean Square Displacement (MSD) for a simulation of $N$ particles under Brownian dynamics with Lennard-Jones interaction between them with or without ...
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0answers
55 views

Radial Hartree and exchange-correlation potentials

According to [1] the one-dimensional Kohn-Sham equation is given by $$ \left( -\frac{1}{2} \frac{d^2}{dr^2} + \frac{l(l+1)}{2r^2} + V[\rho;r]\right) rR_{nl}(r) = \varepsilon_{nl} rR_{nl}(r) $$ where $$...
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0answers
46 views

Troullier-Martins pseudopotential with nonzero angular momentum quantum number

According to [1] the Troullier-Martins pseudopotential for quantum number $l$ is computed by $$ V^{\textrm{KB}}_{\textrm{nonlocal},l}(r) = \frac{\vert{}V_{\textrm{nonlocal},l}(r)\Phi^{\textrm{PP},0}_l(...
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1answer
1k views

Conserving Energy in Physics Simulation with imperfect Numerical Solver

I am creating a C++ Physics Simulation where I need to move an rigid body through an acting force field. Problem: simulation does not conserve energy. Quesiton: abstractly, how is conservation of ...
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0answers
62 views

Computation of Troullier-Martins pseudowavefunctions

The computation of Troullier-Martins pseudowavefunctions has been described in [1]. The pseudowavefunction $R^{\textrm{PP}}_l$ is defined by $$ R^{\textrm{PP}}_l(r) = \left\{ \begin{array}{ll} R^{\...
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1answer
120 views

Numerical Solution to Rayleigh Plesset Equation in Python

I have been trying to numerically solve the Rayleigh-Plesset equation for a sonoluminescence bubble in Python. You can read about this phenomenon here: https://iopscience.iop.org/article/10.1088/0143-...
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141 views

Ising model simulation offset critical temperature and interal ernergy

I'm writing a code for the Ising model using WHAM (the weighted histogram analysis method),But it seems to produce critical temperature and internal energy wrong. (newest rewritten code is below) <...
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1answer
89 views

Numerical bottlenecks

On a desktop scale computer, what are the most important bottlenecks (RAM vs. CPU, single vs. multithread) for numerical calculations? I'm specifically most interested in exact diagonalization and ...
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0answers
36 views

How to avoid density getting “deleted” in two way rigid body coupling with LBM CFD?

I've been reading this paper recently, which talks about using Lattice Boltzmann methods and two way coupling. Specifically, it outlines fluid solid coupling, and solid fluid coupling, and how simply ...
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122 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 ...
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0answers
58 views

Using MATLAB to simulate the Ising Model

I am using MATLAB to simulate a 1D Ising Chain. I am running into an issue where when trying to find heat capacity, my system has a tremendous amount of noise. I'll post my code and an image of the ...
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1answer
149 views

Consumer hardware for scientific computing?

I'm interested in problems around probability, statistics, and statistical mechanics, and often I find it useful to perform simulations to get some sense of the underlying phenomena. Example ...
2
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1answer
45 views

Numerical integration of the dataset of a function

The energy equation for a spherically symmetric system is given by $$\mathscr{E}=\frac{v^2(r)}{2}+\frac{c_s^2(r)}{\gamma-1}+\phi(r)$$ where $\mathscr{E}$ is the total energy, $v$ is the velocity of ...
2
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1answer
73 views

Defining Current Density in a FEM model (MATLAB)

I'm attempting to solve the Poisson equation in 3D for a magnetic vector potential in the presence of a current source. To validate my code, I'm initially looking to reproduce the model described in ...
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1answer
76 views

Evaluating an indefinite integral that has no closed form

I need to evaluate the following indefinite integral: $$I=\int\frac{x^5+2ax^3+a^2x-4a}{x^7+ax^5+2ax^4}dx=\int\frac{x^5+2ax^3+a^2x-4a}{x^4(x^3+ax+2a)}dx$$ The solution that I obtained while ...
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1answer
46 views

Smoothed Particle Hydrodynamics: Weird clustering of particles. Is that normal?

I implemented a rather simple SPH simulation using a cubic-spline-kernel and a simple non-iterative pressure solver as described in this PDF in equation 9. I followed algorithm 1 of that paper (...
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0answers
29 views

solving electron motion in undulator by Boris method

I am trying to use Boris scheme to solve the electron trajectory in undulator. The undulator field I used is: $$B_x = b_0\sin(2\pi \tfrac{z}{\lambda_u})$$ where $b_0 = \dfrac{2\pi c_{0}K}{q m_{e} \...
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1answer
140 views

Runge-Kutta fourth order method. Integrating backwards

I am using a Runge-Kutta fourth order method to solve numerically the usual equation of motion of a background scalar field in curved spacetime with a quartic potential: $\phi^{''}=-3\left(1+\frac{H^{...
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1answer
113 views

For a determined (known) Space charge density, what are the conditions to obtain the Electric potential/field distribution? (COMSOL, MATLAB)

Theoretic part From the theory, in Electrostatics inside a real dielectric material between real conductors, in a simple 1D plane geometry between points $P1$ and $P2$, according to the current ...
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1answer
70 views

Manual for library Libxc

Where can I find the manual for software library Libxc for exchange-correlation functionals? Links with domain www.tddft.org don't work.
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1answer
54 views

Should the derivative of an array be calculated array by array or element by element in CFD codes?

I am making my own finite difference computational magnetohydrodynamic code in Fortran 90. Looking at other codes they appear to calculate for example their $x$-derivatives, bb of their variables, e.g....
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0answers
114 views

Heisenberg Model python : Specific heat capacity for spin 2

I have the correct plot for specific heat capacity when I am using the formula which is $C_V$ = differentiation of entropy with respect to temperature. However, When I try to calculate $C_V$, by using ...
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0answers
36 views

Pseudospectral method for Rayleigh-Benard with constant temperature gradient

$$ \nabla\cdot \mathbf{u} = 0 \\ \frac{\partial \mathbf{u}}{\partial t}+\left(\mathbf{u}\cdot \nabla\right)\mathbf{u} = -\nabla p+\nu\nabla^2\mathbf{u}+\alpha g\theta\mathbf{e}_z\\ \frac{\partial\...
2
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0answers
38 views

What is the best methodology for physics simulators of large floating base rigid body systems?

I want to implement a physics simulator for large floating base rigid body systems from scratch. The Rigid Body Dynamics Systems (RBD) should typically have the following characteristics: About ~50 ...
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1answer
188 views

Problem concerning a part of a simulation for the Ising Model

I was wondering if anyone could help me with a simulation in Python (there is a small part of the code where I have a question) about the Ising model. First, I wanted to get the magnetization $M$ ...
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48 views

Simulate friction arround steady-state point

When simulating a friction dynamic system, I have come to a problem when approaching steady-state. In the example below, a box moves along a surface with a certain friction coefficient: ...

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