CASTEP > Tasks in CASTEP > Analyzing CASTEP results > Visualizing volumetric data

Visualizing volumetric data

You can visualize the spatial distribution of electronic charge, electron density difference, electron localization function, and electrostatic potential calculated by CASTEP. In addition, charge densities of particular orbitals and the approximate STM profile for surfaces in a slab supercell geometry can be visualized. The relevant data from the CASTEP results files are used to add a field to the model. This field can be visualized in a variety of ways (direct field visualization, isosurfaces, slices, etc).

Electronic charge

Materials Studio uses the information stored in the CASTEP binary output file to create a field that corresponds to the electronic charge. When you analyze a spin-polarized calculation, you can create additional separate fields for the density of spin-up (alpha) or spin-down (beta) electrons, as well as a field for the spin density (the difference between the density of alpha and beta electrons). The latter field allows you to visualize the spatial distribution of the magnetic moment in a spin-polarized system.

Maxima in the electronic density field correspond to interatomic bonds or to the position of atoms that have semicore states which are explicitly treated as valence. When there are no semicore states in the system (this can be verified by analyzing the atomic charges displayed on the Potentials tab of the CASTEP Electronic Options dialog), the density will display minima at the positions of atomic nuclei. This is to be expected in the pseudopotential formalism.

To create a density field

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select Electron density from the list of properties.
  3. Ensure that the 3D Atomistic document to be analyzed is the active document.
  4. For spin-polarized calculations, select the type of field required from the Density field dropdown list.
  5. Optionally, check the View isosurface on import checkbox to automatically create an isosurface when the density field is imported.
  6. Click the Import button.

You also have the option of creating a plain text file which contains the values of charge (and spin, when appropriate) density on a regular grid along three lattice vectors. The file has the extension .charg_frm and is hidden by default. Select Tools | Folder Options... in Windows Explorer to open the Folder Options dialog, then select the View tab and click the Show hidden files and folders radio button to reveal the hidden file. The format of the file is self-explanatory:

a       b       c       Charge 
1       1       1    1.8133362740
2       1       1    1.5071161497
3       1       1    1.1111633102
4       1       1    0.9584556846

or, for a spin-polarized calculation:

a       b       c       Charge           Spin  
       1       1       1    1.8130116660    0.0006370238
       2       1       1    1.5068114569    0.0004814296
       3       1       1    1.1108593919    0.0002249406
       4       1       1    0.9580778273    0.0001768619

The charge and spin density in the .charg_frm file are in the same units as those used by CASTEP during calculations. The values are normalized to the number of electrons per cell. The density fields displayed in the 3D model are, however, normalized to the number of electrons per Å3.

To create a plain text density file

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select Electron density from the list of properties.
  3. Click the Save density to file button.

Electron density difference

Materials Studio provides the option of generating the electron density difference in two different ways:

The former option produces a density difference field which shows the changes in the electron distribution that are due to formation of all the bonds in the system. This object is appropriate for bulk solids to illustrate the charge redistribution due to chemical bonding.

The latter option generates a density difference field which effectively corresponds only to the formation of bonds between atoms in different sets and to charge redistribution within the sets that is due to the presence of other sets. This property is useful to describe such processes as bonding of molecule(s) to external and internal (for example, zeolites) surfaces or creation of large molecules from smaller fragments.

To create a density difference field

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select Electron density difference from the list of properties.
  3. Ensure that the 3D Atomistic document to be analyzed is the active document.
  4. Use the Use atomic densities checkbox to request the density difference with respect to a linear combination of the atomic densities. The density difference with respect to the sets of atoms will be produced when this checkbox is unchecked.
  5. Optionally, check the View isosurface on import checkbox to automatically create an isosurface when the potential field is imported.
  6. Click the Import button.
  7. A field is created in the model; its name is either "CASTEP density difference from atoms" or "CASTEP density difference from sets", depending on whether the Use atomic densities checkbox is checked.

Analysis based on atomic densities requires the presence of a binary file with the extension .chdiff; analysis based on sets of atoms requires that for each set of input files, seed_Subset*.*, there are binary files with the extension .check present. The Import button is disabled if the files required for the current setting of the Use atomic densities checkbox are not present in the results folder.

Electron localization function

Materials Studio uses the information stored in the CASTEP binary output file to create a field that corresponds to the localization of electrons.

To create an electron localization function field

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select Electron localization function from the list of properties.
  3. Ensure that the 3D Atomistic document to be analyzed is the active document.
  4. Optionally, check the View isosurface on import checkbox to automatically create an isosurface when the density field is imported.
  5. Click the Import button.
  6. A field is created in the model, named "CASTEP electron localization function".

SCF local potential

Materials Studio uses the information stored in the binary .cst_esp file to create a field that corresponds to the local part of the Kohn-Sham potential. In fact, the data in the file correspond to minus a Kohn-Sham potential. Thus, this field is closely related to the electrostatic potential used in quantum chemistry programs, where it represents the electrostatic energy of a proton at a given point. The units of the potential are eV/electron.

The local SCF potential analyzed in Materials Studio includes all the DFT contributions, except for the nonlocal part of the pseudopotential: the Hartree term, the local pseudopotential term, and the exchange-correlation term. This potential can be used to analyze important solid-state properties such as band offsets and work function (the latter is a specific case of the band offset calculation where one of the materials is a vacuum). An excellent description of the formalism for band offset calculations based on CASTEP results is given by Al Allak and Clark (2001).

To create a local potential field

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select Potentials from the list of properties.
  3. Ensure that the 3D Atomistic document to be analyzed is the active document.
  4. Select the type of field required from the Potential field dropdown list.

    Materials Studio currently supports only the local SCF potential field type.

  5. Optionally, check the View isosurface on import checkbox to automatically create an isosurface when the potential field is imported.
  6. Click the Import button.

Orbitals

Materials Studio uses the information stored by CASTEP in a binary .check file to create a field that corresponds to any of the orbitals in the system. In this context, the orbital is the square of the absolute value of the wavefunction for a given electronic band, summed over all k-points. A band is defined by the position of its eigenvalue in the ordered list of electronic energies at each k-point. For example, orbital (or band) number 3 is obtained by summation over all k-points of the wavefunctions with the third lowest energy. The sum of the "orbital densities" obtained in this way gives the total electron density of the crystal.

Because of the size of the .check file orbital analysis is only available if orbitals are explicitly requested.

The Filter dropdown list, which becomes available on the CASTEP Analysis dialog when Orbitals is selected from the list of properties, allows you to control which orbitals are displayed in the table:

For non-spin-polarized calculations, this option is not available.

The orbital analysis table provides you with a list of eigenvalues and information about each orbital. The list of eigenvalues starts with the lowest energy orbital. The accompanying information includes:

In a non-spin-polarized calculation, all orbitals are labeled +.

You can artificially change the band gap value for insulators or semiconductors by using the scissors operator. This parameter effectively describes the difference between the theoretical and experimental band gap values. When the experimental value is known, you can perform a band structure calculation to find the theoretical band gap. Then, simply set the scissors operator to the difference between the two values. The eigenvalues of the conduction band states displayed in the scrollable list will be shifted upward by the value of the scissors operator.

To create an orbital field

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select Orbitals from the list of properties.
  3. Ensure that the 3D Atomistic document to be analyzed is the active document.
  4. From the scrollable list, select the row(s) corresponding to the orbital(s) you wish to display.

    Multiple selections are allowed. To select more than one orbital, hold down the SHIFT key and click on the first and last orbitals in the block you want to select, or hold down the CTRL key and click to select orbitals individually.

  5. Optionally, check the View isosurface on import checkbox to automatically create an isosurface when the potential field is imported.
  6. Click the Import button.

STM profile

CASTEP models the scanning transmission microscope (STM) profile by representing it as an isosurface of the electron density generated only by states at a certain energy away from the Fermi level. The distance from the Fermi level corresponds to the applied bias in actual STM experiments. Positive bias corresponds to the imaging of empty (conduction) states, while negative bias produces images of occupied (valence) states. This approach neglects the actual geometry of the STM tip and makes use of the Tersoff-Hamman approximation for tunneling transport (Tersoff and Hamman, 1985).

STM profile visualization makes sense only for models that represent surfaces in the slab supercell geometry. In addition, information about charge density at a distance from the surface is likely to be inaccurate as a result of the DFT failing to reproduce the asymptotics of the wavefunction decay into a vacuum.

Because of the size of the .check file STM analysis is available only if orbitals are explicitly requested.

Visualization of the images created by conduction band states requires that the calculation was performed with an increased number of empty bands. The recommended procedure is to use electronic density of states (DOS) calculations and specify a sufficiently high number of empty states.

To create an STM profile

  1. Choose Modules | CASTEP | Analysis from the menu bar to open the CASTEP Analysis dialog.
  2. Select STM profile from the list of properties.
  3. Ensure that the 3D Atomistic document to be analyzed is the active document.
  4. Specify the STM bias value.
  5. Optionally, check the View isosurface on import checkbox to automatically create an isosurface when the potential field is imported.
  6. Use field visualization tools to create an isosurface that represents the STM profile.
  7. Click the Import button.

Field visualization

Materials Studio provides a number of tools for field visualization. They are accessed via the Volume Visualization toolbar and Field, Isosurface, and Slice tabs on the Display Style dialog.

The Volume Visualization toolbar provides access to the Volumetric Selection dialog, which enables you to specify the field to be visualized and set visibility attributes for fields, slices, and isosurfaces. This toolbar also contains controls for creating new isosurfaces and slices, including the shortcuts for orienting the slice based on either the cell axes or the coordinates of selected atoms. The Color Maps dialog, which can also be accessed from the Volume Visualization toolbar, provides control over the coloring of volumetric objects (it also provides useful shortcuts for determining the minimum and maximum values of the field).

The Field tab of the Display Style dialog allows you to visualize the field directly using either the Dots or Volume display styles.

The Isosurface tab of the Display Style dialog allows you to alter the visualization style of a selected isosurface, change its isovalue, or use another field for color mapping.

The Slice tab of the Display Style dialog allows you to alter the visualization style of a selected slice.

The volumetric visualization tabs on the Display Style dialog are displayed only if an object of the relevant type is present in the active document. If a field, isosurface, or slice is selected, for example by using the Volumetric Selection dialog, the volumetric visualization tabs that are not relevant to the selection will be removed from the Display Style dialog.

Field visualization in Materials Studio fully supports periodic display. You can use the Field tab on the Display Style dialog to change the range of a field to display more or less than one unit cell of a structure.

The default settings for field visualization result in the fields being displayed over one unit cell of a structure. Use the In-Cell display mode for the lattice (accessible from the Lattice tab of the Display Style dialog) to make sure that the field is positioned around the displayed atoms.

See Also:

Analyzing CASTEP results
Electron density selection - CASTEP Analysis dialog
Electron localization function selection - CASTEP Analysis dialog
Potentials selection - CASTEP Analysis dialog
Orbitals selection - CASTEP Analysis dialog
STM Profile selection - CASTEP Analysis dialog

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