Step 3 - Set up Basic Processing

We’ll now create two processing layers to handle the evolution of the configuration and the calculation of radial distribution functions and structure factors.

The Evolution Layer

We’ll use the standard molecule evolution layer for our system:

Layer ⇨ Create ⇨ Evolution ⇨ Standard Molecular (MC/MD)

The new layer contains the following modules:

Module	Purpose
MolShake	Performs standard Monte Carlo moves on individual molecules
MD	Performs a number of molecular dynamics steps, evolving the system according to Newton’s equations of motion
Energy	Calculates the total energy of configurations

Monte Carlo simulation via the MolShake module will be the principal way our system moves and evolves, translating and rotating whole molecules but keeping the internal geometry of those molecules constant. The molecular dynamics run is critical for water (and, indeed, any molecular system) because it is this that will relax and evolve the intramolecular degrees of freedom in our molecules and give us realistic sampling of our bonds and angles. We don’t need this to happen every iteration of the simulation, so the frequency of the MD module is set to 5 by default.

g(r) and Structure Factors

We have neutron-weighted experimental data, so we need a layer to calculate RDFs and neutron S(Q):

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

First we need to set the instrumental broadening in the SQ module:

Click on the SQ module to display its options

Set the QBroadening to OmegaDependentGaussian with a FWHM of 0.02

This broadening is a known parameter of the SANDALS instrument on which the experimental data were collected.

For generality, some of Dissolve’s broadening functions refer to ‘omega’, which should be taken to mean the reciprocal space axis (in this case, ‘Q’).

Next, we will set up our calculation of the weighted structure factors. Since a NeutronSQ module calculates the partial and total structure factors for a single isotopic composition, we will need to add two more since we have three reference datasets.

Show the module palette for the layer by clicking Show Available Modules at the very bottom of the module list

Drag a NeutronSQ module from the list of available modules, placing it after the existing NeutronSQ module. Alternatively, double-click the NeutronSQ entry in the list of available modules to append one to the current list of modules

Add another NeutronSQ module, ensuring all three are after the SQ module

Note that each of the new NeutronSQ modules has a unique name (NeutronSQ, NeutronSQ01, and NeutronSQ02) - it is a requirement that modules within Dissolve can be uniquely identified by their name. We’ll now give the modules sensible names that describe our three datasets, and set the isotopologues and reference data files.

H₂O

Click on the first NeutronSQ module (“NeutronSQ”) to display its options

Change its name from “NeutronSQ” to “H2O”

In the Reference Data settings group, for the Reference keyword select the file “SLS18498-H2O.mint01” and set the format of the data to mint

D₂O

Click on the second NeutronSQ module (“NeutronSQ01”) to display its options

Change its name from “NeutronSQ01” to “D2O”

In the Isotopes & Normalisation section click the button for the Isotopologue option - it will currently say <Default to Natural>

Press the Species button to add a new isotopologue for each species present

Change the isotopologue from Natural to Deuterated

In the Reference Data settings group, for the Reference keyword select the file “SLS18502-D2O.mint01” and set the format of the data to mint

HDO

The HDO sample is a little different in respect of the isotopologue specification. In order to get the 50:50 mix we will basically add two isotopologues for the water species - one H₂O and one D₂O. Each will have the same relative weighting of 1.0. Importantly, we must also tell the module that the HW atom type is exchangeable - otherwise, the weighting of the intramolecular terms will be incorrect as, in effect, we will simulate a mix of distinct H₂O and D₂O molecules, which in reality is not what was measured since the hydroxyl hydrogens undergo fast exchange and appear as a mixture on the timescale of the neutron measurements.

As a general rule, any alcoholic or amine hydrogen is exchangeable.

Click on the third NeutronSQ module (“NeutronSQ02”) to display its options

Change its name from “NeutronSQ02” to “HDO”

In the Isotopes & Normalisation section click the button for the Isotopologue option - it will currently say <Default to Natural>

Press the Species button to add the natural isotopologue for the water species

Select the Water species

Click the Isotopologue button to insert another isotopologue (the next unused isotopologue will be added - in this case, the Deuterated one)

In the Isotopes & Normalisation section click the button for the Exchangeable option - it will currently say <None>

Tick the HW atom type in the list

In the Reference Data settings group, for the Reference keyword select the file “SLS18502-HDO5050.mint01” and set the format of the data to mint

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