Configuration Block
Overview
A Configuration block provides a complete description of an atomic / molecular system - e.g. a liquid, crystal, glass, or mixture thereof. A definition of how this system should be created is constructed in a subsection called the ‘generator’ - within that section, references are made to the species present in the configuration. As such, they must have already been defined in one or more Species blocks before the Configuration block in the input file.
The block keyword itself takes a single (required) argument - the name of the configuration. This name is used to reference the configuration when, for example, specifying module targets.
Keywords
| Keyword | Arguments | Default | Description |
|---|---|---|---|
CellDivisionLength |
double |
7.0 |
Set the side length, in Angstroms, of sub-cell regions into which the configuration’s unit cell will be partitioned for the purposes of near-neighbour calculation. The actual side length used to partition the cell will likely differ from the supplied value, in order to ensure full coverage of the whole unit cell volume. |
EndConfiguration |
– | – | Indicates the end of the current Configuration block. |
Generator |
Generator |
– | Specifies a stepwise Generator able to generate the unit cell and contents of the configuration. The generator is called before the main simulation loop begins, unless an existing snapshot of the configuration has been loaded in from a restart file |
InputCoordinates |
CoordinatesFileAndFormat |
– | Load atomic coordinates from the specified file and format. The Generator procedure is still used to construct the initial contents in terms of species etc., but the coordinates of the atoms are subsequently overwritten by those from the file. |
SizeFactor |
double |
1.0 |
Factor by which to temporarily scale the unit cell and molecule centres of geometry. This option is typically used to remove overlaps between molecules containing ring structures, which would otherwise become interlocked for the duration of the simulation. If greater than 1.0, the intermolecular energy is assessed at the beginning of each main loop iteration. If this energy is negative, the size factor is reduced by a predefined factor. |
Temperature |
double |
300 |
Temperature of the configuration in Kelvin. |
Example
Configuration 'Liquid'
Generator
Box
Lengths 1.0 1.0 1.0
Angles 90.0 90.0 90.0
EndBox
Add
Species 'SpeciesA'
Population '200'
Density '0.95' g/cm3
EndAdd
EndGenerator
Temperature 300.000000
EndConfiguration
Generator Examples
Random One-Component System
Simple one-component system, e.g. a pure liquid, with a set number of molecules randomly added to a cubic unit cell. The size of the cell is not explicitly specified - giving a density value (here, the atomic density in atoms/Å3) to the
Add
node allows it to calculate the required volume for the number of molecules requested.
Generator
Box
Lengths 1.0 1.0 1.0
Angles 90.0 90.0 90.0
EndBox
Add
Species 'Water'
Population '1000'
Density '0.1' atoms/A3
Positioning Random
EndAdd
EndGenerator
Random Two-Component System
Two-component system, e.g. a liquid mixture, with a set number of molecules of the second species, and an implied ratio with the first. Again the size of the final cell is not explicitly stated, and the density units are provided in chemical units of the final mix (g/cm3). All control variables are defined in a separate
Parameters
block at the beginning of the generator.
Generator
Parameters
Parameter N 1000
Parameter ratio 2.0
Parameter rho 0.9
EndParameters
Box
Angles 90.0 90.0 90.0
Lengths 1.0 1.0 1.0
EndBox
Add
Species 'Water'
Population N*ratio
Density rho g/cm3
EndAdd
Add
Species 'Alcohol'
Population N
Density rho g/cm3
EndAdd
EndGenerator