demo2 - Demo#2 Molecular Dynamics for the LJ 6-12...

Info icon This preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
Demo #2: Molecular Dynamics for the LJ 6-12 Potential (Author: G. H. Fredrickson (12/29/99). Force calculation adapted from Allen and Tildesley program F.17. MD algorithm is original Verlet with no potential truncation.) In this demo, we are going to explore the MD method applied to the Lenard-Jones 6-12 potential. We will use the standard reduced units of epsilon for energy and sigma for lengths. Our goal will be to estimate the properties of the fluid at temperatures and densities near T*=1.0, rho*=0.85. Lets begin by defining some parameters for the simulation: n 27;boxl 3.167; timestep 0.005; We now calculate the density and half box dimension: boxl2 boxl 2.;boxl3 boxl n^ 1. 3. ;rho n boxl^3 0.850001 The density is thus equal to our target rho*=0.85 by design. Now, lets initialize the particle positions in the simulation box. We will start with a simple cubic lattice to ensure that no particles are too close initially. Otherwise we might have problems integrating the stiff ODEs. tempcoord Table i,j,k , i, boxl3,boxl3,boxl3 , j, boxl3,boxl3,boxl3 , k, boxl3,boxl3,boxl3 ; This next command, restructures the coordinates into an nx3 list d P titi Fl tt t d 3
Image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
pltcoords : Show Graphics3D PointSize 0.10 ,Table Point coord i , i,1,n , PlotRange boxl2,boxl2 , boxl2,boxl2 , boxl2,boxl2 ; pltcoords Graphics3D Next, we need to choose initial velocities. We could select from a Maxwell-Boltzmann distribution, but it is simpler to just select from a uniform distribution and then let the fluid equilibrate. Since the variance of the distribution of velocities is T* in dimensionless units, lets start with something "hot" to make sure we melt the lattice: randomvel Table Random Real, 3.,3. , i,1,n , j,1,3 ; oldcoord coord timestep randomvel; Define a few other quantities that we will need: dtsq timestep^2; dt2 timestep 2.;niter 60;
Image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern