Step 3 - Set Up the Simulation

Create a Configuration

Let’s now set up a configuration for our simulation. We’ll focus on just the Cu-BTC itself which means we essentially want to create a configuration with one copy of the Cu-BTC species in it, and which takes on its unit cell. Dissolve has a specific option for creating this kind of system:

Configuration ⇨ Create ⇨ Empty framework

Choose the MOF species and press Select

Double-click on the configuration tab’s title and change its name to MOF

And that’s it. Note that the generator for this new configuration has only a single step in it which is to Add the framework species. If you click on this step in the list and look at its control parameters you will see that the BoxAction parameter is Set, meaning that the configuration’s box is set from that defined in the species.

Set up Layers

Since our framework is one big periodic molecule there is no point in trying out Monte Carlo translation and rotation moves on it, so we’ll evolve it with just molecular dynamics.

Layer ⇨ Create ⇨ Evolution ⇨ MD (MD Only)

The MD module in this layer runs every step and for a larger number of steps compared to the one in the standard MC/MD layer.

Finally, we need to calculate our correlation functions:

Layer ⇨ Create ⇨ Correlations ⇨ RDF and Neutron S(Q)

Go to the RDF / Neutron S(Q) tab

Click on the SQ module to display its options

Set the QDelta to 0.01

Set the QBroadening to OmegaDependentGaussian with a FWHM of 0.02

Click on the NeutronSQ module to display its options

Open the Reference Data settings group

For the Reference keyword select the file Empty-CuBTC.mint01 and set the format of the data to mint

We’re changing to a finer binning in $Q$ so our Bragg features have better definition.

Add Bragg Scattering

One thing missing from the standard layers is the calculation of Bragg scattering, so we must add a Bragg module in to this layer.

Show the module palette for the current layer by clicking the Show Available Modules button at the bottom of the module list on the left

Drag a Bragg module from the Correlations category up to the module list, placing it in-between the existing RDF and SQ modules

Select the new Bragg module to show its options

Change the QMax to 5.0

The Bragg module is responsible only for calculating the reflection intensities from a target configuration - we must tell the SQ module to take those intensities and incorporate them into the structure factors:

Go to the RDF / Neutron S(Q) tab

Click on the SQ module to display its options

Open the Bragg Scattering options group

Set the IncludeBragg option to reference the only Bragg module we have (called “Bragg”!)

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