CASTEP > Tasks in CASTEP > Setting up CASTEP calculations > Setting up a calculation on an isolated molecule

Setting up a calculation on an isolated molecule

CASTEP can be used to calculate the electronic structure and to optimize the geometry of isolated molecules as well as of solids. In order to study molecules using CASTEP, it is necessary to treat them as periodic systems by assuming that they are in a box. This can be achieved by creating a supercell containing the molecule of interest. There is no limitation on the shape of the supercell, but the simplest approach is to use a rectangular (or even cubic) supercell with a sufficiently large separation between molecules to eliminate spurious interactions between periodic images.

Since both the properties being investigated and the nature of the molecule itself have an influence on the degree of molecular separation required, it is not possible to give a definitive distance that should be established between molecules in a supercell. As a general rule, a box with dimensions that are 4-5 times the size of the molecule should be sufficient. However, it is still important that you check that the size of your supercell is adequate by investigating the convergence of the properties you are interested in against the molecular separation.

Carrying out a stress analysis is a good way of checking that the molecular separation in a supercell is sufficient to preclude any interactions between periodic images, since the stress value provides a guide as to the size of the cell. Alternatively, you could check the band dispersion: the less dispersion in the valence band, the better the molecular separation in the supercell.

CASTEP is an efficient tool for optimizing the geometry of molecules and also enables you to calculate a range of molecular properties, including:

It is recommended that only the Γ-point is used for electronic calculations on molecular systems. In addition, the all bands/EDFT electronic minimizer is known to be more efficient for studies of isolated molecules in supercell geometry than the density mixing minimizer. Therefore, it is recommended that you change the Electronic minimizer setting to All Bands/EDFT on the SCF tab of the CASTEP Electronic Options dialog when performing such calculations.

Calculations for "molecule in a box" systems that do not require geometry optimization can be sped up if the molecular symmetry is utilized. Use the Find Symmetry tool to find and apply the symmetry of the molecule to the supercell.

To create a molecule in a box

  1. Either import a structure from a pre-existing file or construct a new molecule using the sketching tools in the Materials Visualizer.
  2. Construct a crystal using the crystal building tools in the Materials Visualizer.
  3. If your system does not require geometry optimization, find and impose the symmetry of the system using the Find Symmetry tool in the Materials Visualizer.
See Also:

Setting up CASTEP calculations
Setting electronic options
Setting up a geometry optimization
Requesting electronic, structural, and vibrational properties
CASTEP Energy task
CASTEP Geometry Optimization task
CASTEP Properties
CASTEP background theory

Accelrys Materials Studio 8.0 Help: Wednesday, December 17, 2014
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