aboutsummaryrefslogtreecommitdiffhomepage
diff options
context:
space:
mode:
authorJaroCamphuijsen <jjecamphuijsen@gmail.com>2016-04-22 12:13:14 +0200
committerJaroCamphuijsen <jjecamphuijsen@gmail.com>2016-04-22 12:13:14 +0200
commit33c8cdd74075161ff6484cc18b12d18ff9f62dd1 (patch)
treee2f36331b3da54452eec5fb09c0bc3b1a004f40e
parentd98d202e49d4d38531f437b93b76603101e6c49d (diff)
Added some slides and improvements
-rw-r--r--index.html53
1 files changed, 28 insertions, 25 deletions
diff --git a/index.html b/index.html
index 5d856e0..7769376 100644
--- a/index.html
+++ b/index.html
@@ -59,18 +59,6 @@
<p style="text-align:right; margin-top:3px;">
—Richard Feynman</p>
</section>
- <section>
- <h2>Molecular Dynamics</h2>
- <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>
@@ -104,36 +92,51 @@
</section>
</section>
+ <section>
+ <h2>Molecular Dynamics</h2>
+ <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>Physics</h1>
+ <h1>Ingredients</h1>
</section>
<section data-background="Pictures/lj.svg" data-background-size="900px">
- <h1>Lennard-Jones Potential</h1>
+ <h2>Lennard-Jones Potential</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;">
- <div style="align: top";>
- <p>$$ u(r) = 4 \epsilon \left[ \left(\frac{\sigma}{r} \right)^{12} - \left(\frac{\sigma}{r}\right)^6\right]$$</p>
+ <section data-background="Pictures/lj_white.png" data-background-size="900px" style="color: #313532;" data-transition="fade-in">
+ <div align="right" vertical-align="top">
+ <p align="right"> $ u(r) = 4 \epsilon \left[ \left(\frac{\sigma}{r} \right)^{12} - \left(\frac{\sigma}{r}\right)^6\right]$</p>
</div>
- <h1>.<br>.<br>.</h1>
+ <h1><br><br><br><br></h1>
</section>
<section data-background="Pictures/lj.svg" data-background-size="900px">
- <h1>Newton</h1>
+ <h2>Newton</h2>
<ul>
<li class="fragment">$$ F = -\frac{du}{dr} $$</li>
<li class="fragment">$$ F = m a$$</li>
</ul>
</section>
- </section>
- <section>
<section>
- <h1>Verlet Integration</h1>
+ <h2>Verlet Integration</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>
@@ -144,7 +147,7 @@
</section>
<section>
- <h1>A Simple Molecular Dynamics Program</h1>
+ <h2>A Simple Molecular Dynamics Program</h2>
<pre><code data-trim data-noescape>
def main():
init()
@@ -158,7 +161,7 @@ def main():
</section>
<section>
- <h1>Initialization</h1>
+ <h2>Initialization</h2>
<pre><code data-trim data-noescape>
def init():
for i in range(npart):
@@ -169,7 +172,7 @@ def init():
</section>
<section>
- <h1>Force Calculation</h1>
+ <h2>Force Calculation</h2>
<pre><code data-trim data-noescape>
def force(f, en):
for i in range(npart - 1):