interactiveMD/index.html at gh-pages · sunsistemo/interactiveMD · GitHub

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<!doctype html>
<html>
  <head>
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    <title>Interactive Molecular Dynamics</title>

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  <body>
    <div class="reveal">
      <div class="slides">
        <section data-background-iframe="title_background.html">
          <h1>Interactive Molecular Dynamics</h1>
          <h3>Daniel V. Schroeder</h3>

          <p><small>Jaro Camphuijsen & Rahiel Kasim</small></p>
        </section>

	<section>
            <h1> Overview </h1>
            <ul>
                <li>Introduction</li>
                <li>Goal</li>
                <li>Molecular Dynamics</li>
                <ul>
                  <li>Ingredients</li>
                  <li>A Molecular Dynamics Program</li>
                </ul>
                <li>Interactive MD</li>
            </ul>
        </section>
        <section>
            <section>
                <h1>Introduction</h1>
            </section>
            <section data-background="Pictures/apocalypse.jpg">
                <blockquote style="width:1000px; margin-bottom:0px; background-color: #272b23; opacity: 0.85;">
                “If, in some cataclysm, all of scientific knowledge were to be destroyed,
                and only one sentence passed on to the next generation of creatures, what statement would contain
                the most information in the fewest words?  I believe it is the <i>atomic hypothesis</i>
                (or the atomic <i>fact</i>, or whatever you wish to call it) that <i>all things are made of
                atoms—<i></i>little particles that move around in perpetual motion, attracting each
                other when they are a little distance apart, but repelling upon being squeezed
                into one another.</i>”
                </blockquote>
                <p style="text-align:right; margin-top:3px;">
                —Richard Feynman</p>
            </section>
        </section>

        <section>
            <section>
                <h1>Goal</h1>
            </section>
            <!-- <section data-background-iframe="MDstep1bg.html"> -->
            <section data-background="Pictures/lagrangian.png">
                <h3>Disadvantages of Conventional Education</h3>
                <ul>
                    <li class="fragment">No physics, only mathematics</li>
                    <li class="fragment">Only ideal gasses, equilibria, thermodynamic limit</li>
                </ul>
            </section>

            <section>
                <h3>Why Interactive MD</h3>
                <ul>
                    <li class="fragment">
                        Increase qualitative physical understanding
                    </li>
                    <li class="fragment">
                        Perform experiments on inaccessible systems
                    </li>


            </section>
        </section>
        <section>
            <h1>Molecular Dynamics</h1>
            <ol>
                <li class="fragment">Position your atoms</li>
                <li class="fragment">Evolve according to Newton</li>
                <li class="fragment">Wait until it reaches equilibrium</li>
                <li class="fragment">Start measuring $\left(E_\text{kin}, E_\text{pot}\right)$</li>
                <li class="fragment">Compute quantities $\left(P, T, \dots\right)$</li>
                <li class="fragment">Take the time average</li>

            </ol>
        </section>

        <section>
          <section>
            <h1>Ingredients</h1>
          </section>

          <section data-background="Pictures/lj.svg" data-background-size="900px">
            <h2>Potential: Lennard-Jones</h2>
            $$ u(r) = 4 \epsilon \left[ \left(\frac{\sigma}{r} \right)^{12} - \left(\frac{\sigma}{r}\right)^6\right]$$
          </section>

          <section data-background="Pictures/lj_white.png" data-background-size="900px" style="color: #313532;" data-transition="fade-in">
            $ u(r) = 4 \epsilon \left[ \left(\frac{\sigma}{r} \right)^{12} - \left(\frac{\sigma}{r}\right)^6\right]$
          </section>

          <section data-background="Pictures/lj.svg" data-background-size="900px">
            <h2>Force: Newton</h2>
            <ul>
              <li class="fragment">$$ F = m a$$</li>
              <li class="fragment">$$ F = -\frac{du}{dr} $$</li>
            </ul>
          </section>

          <section>
              <h2>Integration: Velocity Verlet</h2>
              \begin{align}
              r \left(t+\Delta t \right)&=r(t) + v(t) \Delta t + \frac{f(t)}{2m}\Delta t^2\\
              \quad\\
              v \left(t+\Delta t \right)&=v(t) + \frac{f(t+\Delta t) + f(t)}{2m}\Delta t
              \end{align}
          </section>

        </section>

        <section>
          <section>
            <h1>Building a Molecular Dynamics program</h1>
          </section>

          <section>
            <h2>A Simple Molecular Dynamics Program</h2>
            <pre><code data-trim data-noescape>
def main():
    init()
    t = 0
    while (t < tmax):        # MD loop
        force(f, en)         # determine forces
        integrate(f, en)     # integrate equations of motion
        t = t + delt
        sample()             # sample averages
            </code></pre>
          </section>

          <section>
            <h2>Force Calculation</h2>
            <pre><code data-trim data-noescape>
def force(f, en):
    for i in range(npart - 1):
        for j in range(i + 1, npart):  # loop over all pairs
            xr = x[i] - x[j]
            xr = xr - box * round(xr / box)
            r2 = xr ** 2
            if (r2 < rc2):      # test cutoff
                r2i = 1 / r2
                r6i = r2i ** 3
                ff = 48 * r2i * r6i * (r6i - 0.5)  # L-J potential
                f[i] = f[i] + ff * xr
                f[j] = f[j] - ff * xr
                en = en + 4 * r6i * (r6i - 1) - ecut
    return
            </code></pre>
          </section>

        </section>

        <section>
            <iframe data-src="mdApplet.html" width="770" height="700" style="overflow:hidden;"></iframe>
        </section>

        <section data-background-iframe="title_background.html">
          <h1>Questions...?</h1>
          <p class="fragment">Follow the course <b>Understanding Molecular Simulation</b> in Period 3
        </section>
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