Step 3 - Set Up the Simulation
Create a Configuration
When importing the original CIF file a configuration was automatically created, so in this example we’re ready to go. It might be instructive to look at the nodes in the generator, specifcally the
Add
node for the framework species. If you 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
OmegaDependentGaussianwith a FWHM of0.02
Click on the
NeutronSQ module to display its options
For the Reference keyword in the Reference Data settings group, select the file
Empty-CuBTC.mint01and set the format of the data tomint
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 button at the bottom of the module list on the left
Drag a
GR and
Select the new
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
Click on the
Find the Bragg Scattering options group and set the IncludeBragg option to reference the only