Interfacial energy tool (IET)

ASAP provides a flexible GUI to facilitate all the steps involved in the workflow of computing the energy (single-point calculation) of a set of systems built out of two subsystems placed at different relative distances (d).

An Interfacial energy tool (IET) project starts defining the two atomic structures of the subsystems. We refer the user to section Structure Modeling in ASAP for further information on the ASAP structure builder/viewer interface.

To create a new IET project, select two existing projects in the project tray containing the desired subsystems,

then, right-click to select the option Merge two structures to merge the two selected subsystems into one.

The widget offers the possibility of visualising the system from different views (View angles).

You can decide to Keep constrains of the existing systems, Fix or Release the position of the atoms of the first and second subsystem.

You can also indicate the relative distance (in x, y or z direction) between the two subsystems.

Additionally, you can also choose the Unit cell: Unit cell of the first subsystem, Unit cell of the second subsystem, No unit cell or Minimal unit cell. Finally, thick the wrap atoms into the unit cell checkbox to bring the coordinates back to the unit cell. The periodicity of the current unit cell is assumed.

Press the OK button to merge the two systems following your specifications, and edit the type of the project by selecting Interfacial energy tool from the list of possible project types implemented in ASAP.

ASAP will open a window showing the composition of the interface:

Press the Yes button to proceed.

Then click on the Parameters icon to open the Parameter widget. Notice that for this type of project, only settings options are available.

The settings widget associated with a IET type of project offers the following options:

• Energy definition: The available options are

  • Total energy: Total energy of the system provided directly by the calculator.

  • Interaction energy: The interaction energy defined as

    \[\Delta E = E(AB)_{ab} - E(A)_{ab} - E(B)_{ab}\]

    is calculated. \(E(AB)_{ab}\) is the energy of the whole system (\(AB\)) while \(E(A)_{ab}\) and \(E(B)_{ab}\) are the energy of the first and second subsystems, respectively, computed using a mixed basis set (ghost atoms).

  

• Distances, out of plane: Minimum and maximum relative distance between the two subsystems.

• Shifts, in-plane: Number of points to be sampled on the surface in the x and y directions. Check the tick-box Randomise to make a random sampling of the surface.

Press the Export to PDBs… button to export the set of built systems as a set of PDB images.

Press the OK button to close the IET widget once the parameters are properly set.

Click on the Calculator icon to select the computational engine to be used during geometry optimisation. We refer the user to chapter Calculators for further information on the available calculators in ASAP.

Click on the Run icon to open the Run widget.

Then click on the Run button to submit the previously defined set of calculations. We refer the user to chapter Configure ASAP runners for further information on the computational resources configuration in ASAP.

After submitting a job (run), the Calculator output tab in the Run widget shows the complete calculation output in real time.

In addition, the Task output tab in the Run widget shows relevant information on the IET output in real-time. It indicates the images for which the energy has already been computed.

Interfacial Energy Tool workflow: Analysis

When the calculation is completed, select Exit and analyse to open the analysis widget.

The analysis widget shows the visualisation of the energy for each of the calculated systems.

Click the Fit check box to fit the curve to the Morse potential equation and to compute the Morse parameters.

Press the Definition button to get information on the interatomic interaction Morse potential model.

Click the Definition lines check box to visualise the relevant quantities in the figure.

Select View current image… to view the current image in three dimensions. And select View all in 3D… to visualize all IET images in three dimensions.

Press the Export energies… button to export the data from the figure to a text file format.

Press the Export to PDBs… button to export the set of built systems as a set of PDB images.

Right-click on top of the figure to:

• Save figure as…. The supported formats are .pdf, .png, .jpg, .jpeg, .ps, eps, svg.

• Open in Matplotlib…. Matplolib library allows the user an interactive visualisation of the figure (scale axis, zoom on specific X and Y values…).

• Save a Matplotlib script as…. Save the Matplotlib script used to plot the figure.