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    A5: Problem On Kinetic Monte Carlo and Molecular Dynamics

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    RohitThakran
    This document presents two problems involving kinetic Monte Carlo and molecular dynamics simulations. Problem A involves using kinetic Monte Carlo to model the breakage of particles of different volumes over time and analyze the resulting particle size distributions. Problem B involves performing molecular dynamics simulations of inert gas atoms in a box using the Lennard-Jones potential. It involves (1) equilibrating the system at constant temperature, (2) comparing initial configurations, and (3) analyzing mean squared displacements and diffusivity as a function of temperature.

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    A5: Problem On Kinetic Monte Carlo and Molecular Dynamics

    Uploaded by

    RohitThakran
    25 views2 pages
    This document presents two problems involving kinetic Monte Carlo and molecular dynamics simulations. Problem A involves using kinetic Monte Carlo to model the breakage of particles of different volumes over time and analyze the resulting particle size distributions. Problem B involves performing molecular dynamics simulations of inert gas atoms in a box using the Lennard-Jones potential. It involves (1) equilibrating the system at constant temperature, (2) comparing initial configurations, and (3) analyzing mean squared displacements and diffusivity as a function of temperature.

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    A5_KMC_and_MD

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    This document presents two problems involving kinetic Monte Carlo and molecular dynamics simulations. Problem A involves using kinetic Monte Carlo to model the breakage of particles of different volumes over time and analyze the resulting particle size distributions. Problem B involves performing molecular dynamics simulations of inert gas atoms in a box using the Lennard-Jones potential. It involves (1) equilibrating the system at constant temperature, (2) comparing initial configurations, and (3) analyzing mean squared displacements and diffusivity as a function of temperature.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    25 views2 pages

    A5: Problem On Kinetic Monte Carlo and Molecular Dynamics

    Uploaded by

    RohitThakran
    This document presents two problems involving kinetic Monte Carlo and molecular dynamics simulations. Problem A involves using kinetic Monte Carlo to model the breakage of particles of different volumes over time and analyze the resulting particle size distributions. Problem B involves performing molecular dynamics simulations of inert gas atoms in a box using the Lennard-Jones potential. It involves (1) equilibrating the system at constant temperature, (2) comparing initial configurations, and (3) analyzing mean squared displacements and diffusivity as a function of temperature.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 2

    A5: Problem on Kinetic monte Carlo and Molecular Dynamics

    [Problem A] Kinetic Monte Carlo

    Consider a system consisting of five particles of volumes 1,2,4, 5, and 7. These particles undergo
    breakage, leading to formation of smaller new (daughter) particles. The breakage rate is
    proportional to their volumes with the proportionality constant is unity. You can consider binary
    breakage (resulting into same sized daughter particles) for part (a)-(c).

    (a) Use hand calculations to estimate the particle size distribution after 3 events, based on the
    kinetic monte carlo method.

    (b) Find the state of the system after 30 events using a computer code. Plot the particle size
    distribution after 30 events. Use the same seed for the random number generation.

    (c) Repeat (b) using random numbers generated from different seeds and compare the results.

    (d) If the number of the particles on breakage is more than 2, and the daughter size distribution is
    gaussian (or normal), show from computer calculations that the final particle size distribution (as 𝑡 →
    ∞) of a properly sampled state space, also follows normal distribution.

    1
    [Problem B] Molecular Dynamics calculations

    Consider 10 inert atoms containing inside a box. For students having the last digit of the roll number
    to be odd – consider these atoms to be Argon and for even roll number – Xenon atoms.

    Since, these atoms are neutral and inert, there is no bonded or electrostatic interaction. The only
    (inter-particle) interaction is of the van der Waals nature. The Lennar-Jones 6-12 potential
    parameters for Argon are: 𝜖 = 1 𝑘𝐽/𝑚𝑜𝑙 and 𝜎 = 0.34 𝑛𝑚; while for Xenon: 𝜖 = 1.77 𝑘𝐽/𝑚𝑜𝑙 and
    𝜎 = 0.41 𝑛𝑚. You may assign initial velocities to the atoms corresponding to the T = 200 K. Choose
    the box size (2D) according to the density of the gaseous system at the specified temperature. Apply
    periodic boundary conditions on the sides of the box. The size of the atoms is around 0.2 nm.

    (a) Calculation the equilibrium positions of the atoms in the system until the total potential energy
    of the system changes by less than 0.1% in the subsequent steps. Follow the Newton’s laws of
    motion to calculate the velocity and displacement of the particles. Choose a timestep of the
    integration such the net change in the displacement (sum of the displacements of all the particle) in
    one timestep is less than 0.02𝜎. A rough calculation can be done initially to understand the scale of
    the timestep. You can update (increase or decrease) the timestep with the integration steps, as this
    will make computation faster. Plot the total kinetic and potential energy of the system as a function
    of the simulation time steps.

    (b) What happens to the temperature of the system when the system has reached equilibrium? How
    can you maintain constant temperature during the simulation? [This needs extra reading]. Please
    incorporate and make necessary changes in your calculations, so that the temperature is held
    constant during the simulation. Plot the total kinetic and potential energy of the system as a
    function of the simulation time steps.

    (c) Do you get different equilibrium configurations depending on the initial state of the system? To
    answer this point, please compare the final equilibrium results corresponding to –

    (i) Initial position based on periodic cubic lattice positions, where the inter-particle distance
    is uniform for all the atoms.

    (ii) initial position is randomly distributed following the Metropolis-Hastings algorithm,


    generating an initial random state.

    Based on the initial configuration as described in (i) and (ii), carry out the simulation at constant
    temperature. Report the potential energy and kinetic energy of the system as a function of the
    simulation time steps. Plot the final equilibrium position of the atoms for (i) and (ii).

    (d) Calculate the average (of all the particles) mean squared displacements (MSD) of the molecules
    at different time instants and make a plot of the MSD with time. Estimate the diffusivity (D) of the
    atoms. Repeat your calculations for different temperatures 𝑇 (at least 5 other temperatures), and
    plot diffusivity as a function of T. Can you establish that 𝐷 ~ 𝑇 3/2 ? which is true for gases

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