Water on an aluminum surface

This tutorial will help you to:

• create an aluminum slab
• add a solvent (water)
• run the simulation and see what happens

Step 1: Start ReaxFFinput

Start ADFjobs

Use the SCM → New input menu command

Switch to ReaxFF mode (panel bar ADF → ReaxFF)

Step 2: Creating the surface

Bulk aluminum has an fcc crystal structure, with a lattice constant of about 4.0 Angstrom.

To create the surface, we first build bulk aluminum:

Edit → Crystal → Cubic → fcc

In the dialog that appears:

Select the preset Al

Click the OK button

View → Periodic → Repeat Unit Cells

In your molecule editor screen you should see a picture of the bulk aluminum structure. The unit cell contains one atom. As ReaxFF input by default does not show repeated cells, it had to be turned on explicitly. Otherwise you see only the single atom in the unit cell.

Now create the surface:

Edit → Crystal → Generate Slab...

In the Dialog window:

Check the Cartesian check box

Set the number of layers to 3

Click OK

View → Periodic → Repeat Unit Cells

You will see three atoms as it is a three-layer slab.

In this case we do not want just one unit cell, but a much bigger piece of the slab:

Turn off periodic view:

View → Periodic → Repeat Unit Cells

Edit → Crystal → Generate Super Cell...

Put 10, 10, 1 on the diagonal

Click OK

Rotate get a better view

Now we have a real slab of aluminum, three layers thick. Note that the Generate Super Cell command adjusted the lattice vectors to match the new unit cell.

Step 3: Add solvent

The next step is to add water to the system, and make sure that the slab is in the center of the simulation box:

Edit → Builder

Change the third dimension of the lattice vectors to 100.0

Check the Move to center of box box on the line for the Current molecule

Type wa in the line with ‘Fill box with’

Select Water (ADF) from the search results

Specify 2500 copies

Specify a distance of 1.0 Angstrom (this is the minimum distance between the molecules)

Click the Generate Molecules button on the bottom

Make sure the origin is in the center of the box: Edit → Set Origin

Use the View → Periodic → Show Unit Cell command to visualize the box

Rotate to your favorite view

Step 4: Set up the simulation, including a temperature regime

Now we will set up the MD-simulation. We will use the Al-water force field and a Nose-Hoover thermostat with a default damping constant of 100 fs:

Close the Builder by clicking the Close button on the bottom

Click on the folder icon and select the Al-H2O force field

Specify 10000 iterations

From the Method menu, select NVT Nose-Hoover chains

In the simulation we would like something to happen. So we will use a high temperature for water, but try to keep the aluminum cool. Also, we will start with a low temperature MD to relax the initial set-up. This can all be accomplished using a temperature regime, specifying different temperatures for different regions.

For this we first need to define two new regions: one for the aluminum slab, and one for the water. Regions in ReaxFFinput are the same as in the ADF-GUI: they are defined as a collection of atoms. Via the Regions panel you can define the regions:

panel bar Model → Regions

Click once on the select button (the V like button) in the Auto-Generated region

By pressing the select button you have selected all atoms in the ‘Auto-Generated’ region. This region will always contain the atoms that are added by the Builder. Thus, as you can see, all water molecules are selected.

We are going to set up a region for the water molecules, and a region for the aluminum surface:

With the water molecules still selected, press the + button in front of the Regions label

Click and select the text Region_2 and change it into Water

Now we have a region defined that contains all water molecules. Note that the selected atoms (in this case all water molecules) were automatically added to the new region. The + and - buttons add or remove the selected atoms to a region.

Click in the drawing area so it has focus (otherwise the next will select the region name)

Select → Select All

Press the + button in front of the Regions label again to add a new region (containing everything as everything was selected)

Change the name Region_3 to Al

Click the select button in the Water region to select all water molecules

Click the - button in the Al region to remove the water from the Al region

Click in empty space to clear the selection

The different regions are shown with colors. This does make the display a lot slower. You can turn off (or on) this display with the check box in front of the Region names, and you can set visualization style per region:

Uncheck the check box at the left of the Water region line

Press the triangle on the right side of the Al region line, and choose for the Balls And Sticks visualization option

Now we have defined the regions that we need, now set up the temperature regime:

Panel bar Model → Temperature Regime

Press the + button in front of the Regime label twice to add two temperature steps

At iteration 0, we start with an MD simulation at T=0 K:

change the first 298.0 to 0.0 (note this applies to region All which is everything)

At iteration 2000, we set the water temperature to 2000 K, while keeping the aluminum temperature at 0 K:

Change the number of iterations from 10000 to 2000

Press the + button on the right side of the line starting with 2000

Change the first All on the 2000 step to Al, and change its temperature to 0.0 K

Change the second All on the 2000 step to Water, and change its temperature to 2000.0 K

Your temperature regime setup should look like this:

Step 5: Run the simulation

Now we can run our set up:

File → Run

When asked to save, specify Al-water as filename

A warning will be shown regarding a force field problem. Click Ok in the dialog then Yes to save the run script.

Let it run for some time (until iteration 500 or so)

SCM → Movie

View → Molecule → Balls And Sticks

Rotate and zoom to get a good view of the surface

If you look around, you will most likely see many water molecules attaching to the aluminum surface. After some time, you might also see hydrogen atoms distracted from the water molecules, which are now moving around the surface on their own.

You might leave the simulation running to see what will happen. It will take a lot of time though.

If you do not want to wait for the simulation to finish, kill the job:

Bring the ADFjobs window to the front

Make sure your Al-water job is selected (click once on it if not)

Kill it Job → Kill

Close all GUI modules: SCM → Quit All