Generate Surfaces and Surface Properties
CrystalExplorer can generate the following surfaces:
- Crystal Voids
- Electron Density
- Deformation Density
- Electrostatic Potentials
- Molecular Orbitals
- Spin density
One of the most powerful features of CrystalExplorer is the ability to map properties onto surfaces with color. Some of these properties e.g. the electron density property must be chosen when generating the surface but there are a number of built-in properties that are always available to these surfaces. At present only Hirshfeld, Promolecule and Electron Density surfaces can have properties mapped onto them.
For further information see: Surfaces in CrystalExplorer and Surface Properties.
The General procedure for generating surfaces is:
- Using the mouse, select the atoms you want included in the surface. In general you'll want to select a complete molecule, although CrystalExplorer will often allow surfaces to be generated for any selection including single atoms.
- Click the toolbar button to bring up the Surface Generation dialog.
- In the Surface Generation dialog you must choose the surface type, any surface properties and the resolution (quality). Surfaces can be further customised with surface options e.g. the surface's isovalue. Click the OK button to generate the surface.
Some of the surfaces and surface properties are quantum mechanical in nature and require a wavefunction. CrystalExplorer automatically enlarges the Surface Generation dialog when a wavefunction calculation is required.
Wavefunction calculations can be performed with the built-in Tonto program or with Gaussian program. In order for CrystalExplorer to be able to use Gaussian follow these the steps on the "Setting up Gaussian" page. Note: Gaussian is not distributed with CrystalExplorer and must be purchased separately.
All generated surfaces appear in that crystal's surface list. A green tick next to a surface name tells CrystalExplorer to show that surface in the graphics window. By clicking on the green tick, it will be changed to a red cross and the surface will be hidden from view. This is useful if you have many surfaces and only want to keep the display from getting cluttered.
The Surface Controller (located at the bottom right hand side of the CrystalExplorer Window) gives you details about the surfaces and allows you to change features of the surface ― for example, which property is currently mapped on its surface. The Surface Controller has three tabs,
- Options Tab: allows you to set all aspects of the surface, including the property mapped on the surface, the color range for the property, and whether the surface is displayed semi-transparent
- Info Tab: displays information such as the surface area and volume, globularity and asphericity
- Property Info Tab: provides the min, max and mean values of each property mapped on the surface
All Hirshfeld surfaces have the following properties mapped by default:
- None (a monochrome surface; colour can be changed in the Preferences → Graphics dialog)
- Shape index
- Fragment patch (surface patches adjacent to neighbouring surfaces are coloured separately)
Sometimes it is desirable to generate a cluster of molecules with identical Hirshfeld surfaces (and a property mapped on these surfaces). The Clone Surface button performs this function without the need for repeated (and time-consuming) generation of all the surfaces. Once a single Hirshfeld surface has been created it can be copied onto all symmetry-related molecules in the graphics window by clicking on the toolbar button.
Once these surfaces have been generated they exist as separate entities and can be individually decorated with different surface properties.