Surface deposition: Bouncing C₆₀
********************************

ReaxFF Graphene Surface Molecular Dynamics Molecule gun

In this tutorial we will be modeling the impact of a C60 buckyball on
a graphene sheet:

[image]

For the purpose of this tutorial we are going to use the ReaxFF
engine, as it is very fast. However, one can also follow this tutorial
using for example the DFTB engine.


Setting up the geometry
=======================

Let us begin by creating a graphene sheet.

   **1.** Start **AMSinput**.
   **2.** Switch to **ReaxFF**: [image: ADFPanel][image] **→** [image: ReaxFFPanel][image]
   **3.** Click on the **magnifying glass** [image: Search][image]
   **4.** Search for "graphite" and select **C128: Graphite** from the crystal compounds.
 [image]

The graphite cell shown in the viewport on the left consists of four
graphene layers. For our example we need a single layer, so let us
delete the others.

   **1.** **Left click and drag** in the viewport to rotate the graphite cell into an orientation where you can easily see the four layers.
   **2.** Select three of the layers by holding down the **Shift** key using the **Left mouse button** to **draw a selection box** around them in the viewport.
   **3.** Press the **DEL** (or **backspace**) button on your keyboard to delete the selected atoms.
 [image]

In the image above we kept the graphene layer in the xy-plane and
deleted the other three. At the moment we still have periodicity along
the z-axis. We only really a single graphene sheet, so let us just get
rid of this third lattice vector:

   **1.** Switch **Periodicity** from **Bulk** to **Slab**.

We now have a single layer of graphene with an infinite vacuum below
and above. Our graphene sheet is still rather small though: Too small
to shoot something large like a buckyball at it! Let us make it larger
using the super cell tool.

   **1.** Click on **Edit** in the menu bar of the AMSinput window.
   **2.** Select **Crystal → Generate Super Cell**
   **3.** In the pop-up window enter "6", "6" on the diagonal.
   **4.** Click **Ok**.
 [image]

Now that we have a reasonably sized graphene sheet we can insert the
buckyball.

   **1.** Click on the **magnifying glass** [image: Search][image]
   **2.** Enter "buckyball" into the search field and select **C60: Buckyball (ADF)**.
 [image]

The inserted buckyball should automatically be selected. However, it
is currently sitting at the origin of the cell *inside* of the
graphene sheet. We are going to have to move it out of there.

   **1.** Use your **right mouse button** to drag the buckyball above the graphene sheet.
   **2.** Position it above one of the sharp corners of the sheet.
 [image]

The buckyball should now be in a nice place from which we can shoot it
at the center of the graphene sheet. It is time to aim the gun ...

Tip:

  If you accidentally deselected the buckyball, you can reselect it by
  selecting one of the atoms in it and choosing **Select → Select
  Molecule** from the menu bar.


Setting up the molecule gun
===========================

The molecule gun in AMS uses regions to identify which part of the
geometry is the projectile and which is the target. Let's make sure we
have the buckyball (our projectile) in a separate region.

   **1.** Open the **Regions panel** by clicking **Model → Regions**.
   **2.** Select the buckyball by holding down the **Shift** key and dragging a box around it using your **left mouse button** in the viewport.
   **3.** With the selected buckyball, click the **+** button in the **Regions panel** on the right.
   **4.** Confirm that your buckyball is now **highlighted** in the viewport on the left.
   **5.** Rename the newly created region to from "Region_1" to "Buckyball1" by typing in the corresponding text box on the **Regions panel**.
 [image]

Next we need to set up some general aspects of our MD simulation.

   **1.** Switch to the **Main** panel.
   **2.** Select "C.ff" as the **Force field**.
   **3.** Make sure the **Task** is set to **Molecular Dynamics**.
   **4.** Go to the molecular dynamics details panel by clicking [image: MoreBtn][image] to the right.
   **5.** Set the **Number of steps** to "8000".
   **6.** Set the **Sample frequency** to "50".
   **7.** Set **Initial velocities** to **Zero**.
 [image]

This should give us a sufficiently long and smooth trajectory of the
impact.

We will also disable the preservation of the momenta, otherwise the
graphene layer drift towards the incoming buckyball in an attempt to
remove the system's total momentum, which is not what we want. We just
want the graphene layer to remain stationary until the buckyball hits.

   **1.** Switch to the **Model → MD... → Preserve** panel.
   **2.** Untick all the boxes next to **Preserve**.
 [image]

Finally, we need to configure the molecule gun!

   **1.** Click on **Model → MD... → Molecule Gun**.
   **2.** Click on **+** next to **Add Molecules** to add a new projectile.
   **3.** Select our previously set up region "Buckyball1" from the **System** drop-down menu.

As you can see, the molecule gun panel looks relatively complicated.
This is because it supports not only single shots, but also a regular
shooting from randomized positions in random directions. It could, for
example, be used to let many molecules rain down on a surface.
Together with the molecule removal features, this can be used to set
up quite involved simulations.

See also:

  See the molecule gun section in the AMS driver manual for a complete
  overview of the supported options.

In this tutorial we are going to keep things simple and only shoot a
single buckyball at the beginning of the simulation.

   **1.** Set **Frequency** to "1".
   **2.** Set **Start step** to "1".
   **3.** Set **Stop step** to "1".

The last thing we need to specify is the direction and velocity of our
shot. AMSinput uses the vector from one atom to another to define the
shooting direction of the molecule gun. This is very convenient for
us, since we can just use an atom of the buckyball and an atom of the
sheet to define the direction.

   **1.** Select one of the atoms in the buckyball by **left clicking** on it.
   **2.** Add one of the atoms in the center of the sheet to your selection by holding the **Shift** key and **left clicking** it.
   **3.** Click the **+** button next to **Velocity direction**.
   **4.** Set a **Velocity** of "0.05" Å/fs.
 [image]

Warning:

  The order in which the atoms are selected determines the direction
  of the shot! If you select them in the opposite order before
  clicking the **+** button, you will shoot in the opposite direction!

Note:

  The distance between the atoms defining the direction will not
  affect the starting velocity. Their sole purpose is the definition
  of a direction.

Tip:

  If your system does not already contain atoms you can conveniently
  use to define a shooting direction, you can always insert **dummy
  atoms** ("Xx" in the periodic table tool) in convenient locations
  (or use **centroids**). These are not real atoms and will not be
  included in your simulation. They are just used for the setup of
  your calculation in AMSinput.

This concludes the setup of the calculation.


Visualizing the impact
======================

We are now ready to shoot! Let us run the calculation.

   **1.** Click on **File → Save as...** and give it a reasonable job name.
   **2.** Run the calculation with **File → Run**.

The AMSjobs window will come to the front as the calculation starts
running. As ReaxFF is a very fast engine and the system not
particularly big, it should only take a couple of minutes. We can
already visualize our calculation while it is still running.

   **1.** Select your job in AMSjobs by **left clicking on its job name**.
   **2.** Click on **SCM → Movie** to visualize the trajectory.

You can download the movie here if it does not play in your browser.
The saved movie was made using the **File → Save Movie...** command.
If you want to use it you will have to install ffmpeg first.

Your initial velocity was probably not large enough to make the
buckyball penetrate the graphene sheet. You will likely get a
trajectory very similar to the one above. Note how the shock wave in
the graphene starts interfering with itself as it travels across the
periodic boundary conditions. Feel free to go back to AMSinput and
increase the initial velocity of the buckyball. Doubling the velocity
might already be enough to punch a hole into the graphene ...

This concludes the tutorial on the molecule gun in AMS.
