Chapter 4. Usage

Table of Contents

4.1. OVITO basics
4.1.1. Data model
4.1.2. Processing model
4.2. Importing atomistic data
4.3. Working with modifiers
4.4. Rendering
4.5. Exporting atomistic data

4.1. OVITO basics

This section introduces the basics of OVITO that you need to work effectively with the software.

4.1.1. Data model

OVITO uses an object-oriented data model to store atomistic data. The base object is the so-called AtomsObject, which encompasses a single snapshot of the atomistic system. It includes the simulation cell information and the atoms. The per-atom data is again divided into so-called data channels. A data channel is basically an array of values, one for each atom, that stores a single property for all atoms. These per-atom values can be either scalars or vectors or something else (e.g. tensors). OVITO knows a number of pre-defined types of data channels that store commonly used properties, as for example, the mendatory Position data channel, which stores the atomic positions in a 3-component vector. Another important data channel is the Atom Type data channel, which holds the type (i.e. chemical species) of each atom as an integer number.

In addition to the per-atom data, some data channels store parameters and settings that are specific to the data channel type. For example, the Atom Type data channel also stores the display names, colors, and radii of each species. OVITO uses this information to display atoms from each group. These extra control parameters are documented for each standard channel in the data channel reference section of this manual.

OVITO allows the user to define new data channels. This can either happen during import of an input file that contains extra data columns, which the user wants to process in OVITO. Or it can happen later on, when the user performs an operation that generates a non-standard data channel, as for example the Add Expression Channel modifier.

Another term that you'll encounter in this manual and when using the software is the scene. A scene is the complete data you are currently editing in OVITO. It is equivalent to what is called a document in other programs, as for example a word processing software. An OVITO document is three-dimensional space that contains a number of objects that are placed in a certain way. That's why it is called a scene. You can save the complete scene to a file, like in other editing programs, and load it again into OVITO at a later time.

4.1.2. Processing model

When you import a data file produced by your simulation code into OVITO, it is internally represented by an AtomsObject as introduced in the previous section. OVITO uses the information stored in the data channels to display the atoms in the viewports. This data, however, is not static. You can define a sequence of operations that are applied to the data first, before the atoms are rendered by OVITO. These operations are called modifiers in OVITO and are the basic building blocks that you put together to reach a specific goal.

The used-defined sequence of modifiers is called the processing pipeline. First, the AtomsObject is generated from the input file, it is then fed into the pipeline, undergoes transformations while flowing through the pipeline, and is finally handed over to the displaying engine, which generates the image seen by the user. In fact, while working with OVITO, you spend most of the time with adding new modifiers to the pipeline and adjusting their parameters. This manual contains a list of available modifiers.

The modifier concept gives OVITO its great flexibility because, in contrast to a classical workflow, the data is not changed permanently by the modifiers. Instead, you can go back and change parameters of any of the modifiers in the sequence when needed and OVITO will immediately re-evaluate all operations and update the results. Of course, you can also replace the input data of the processing pipeline easily. This is ideal for batch processing of a large number of simulation snapshots, for example.

4.2. Importing atomistic data

Atomistic data may come from different sources and is stored in different file formats. OVITO can directly import a variety of file formats written by several simulation packages:

You import atomistic data into OVITO via the import function. Choose FileImport from the main menu or use the key shortcut Ctrl+i. This will open a file selector dialog that lets you choose the file to import. You have to specify the correct file format by selecting an entry in the drop-down list at the bottom of the dialog.

Note

Importing an atoms file will completely replace the current scene. That is, you will loose your current modifier sequence. If you just want to replace the input data and keep your modifier sequence then you have to change the input file in the properties panel of the import object.

After selecting the input file another dialog box might show up, depending on the select file format. Some file formats like the LAMMPS dump format or the XYZ format can contain an arbitrary number of data columns in any order. Thus, when importing such a file you will have to specify the mapping from the data columns in the input file to OVITO's internal data channels.

The LAMMPS dump import function and the XYZ import function support sequences of input files with multiple snapshots. See their documentation sections for more info.

4.3. Working with modifiers

Figure 4.1. The Modify tab

The Modify tab


Modifiers are added to the processing pipeline on the Modify tab of the command panel. This tab is labeled with the icon and contains three main sections:

  • A drop-down listbox labeled Modifier List, which lets you add new modifiers to the current processing pipeline.
  • A large listbox that shows the processing pipeline of the currently selected scene object.
  • The properties panel, which shows the parameters of the currently selected entry of the processing pipeline.

Note

The Modify tab lets you edit the processing pipeline of the selected scene object. After importing an atomistic data file your scene contains exactly one scene object: the simulation box including the atoms (the so-called Atoms Object). It is selected by default as indicated by the white color of the simulation box. If you click somewhere next to the simulation box in the viewports then it becomes unselected and the controls on the Modify tab become disabled. Then click into simulation box to select it again.

After importing atoms the processing pipeline listbox contains a single entry named Input File followed by the name of the imported file. This entry denotes the source of the processing pipeline, i.e. the origin of the atomistic data that is fed into the processing pipeline. When you select this entry you can edit the properties of the as-imported data in the properties panel below the listbox. What you see here is the parameter panel of the Import Atoms Object. It lets you perform several important things, e.g. replacing the input file, changing atom colors, and changing the default display radius for atoms. See Section 5.4 for more details.

You can add a new modifier to the initially empty processing pipeline by choosing an entry from the drop-down box labeled Modifier List. The new modifier will be inserted into the pipeline above the selected entry. Note that the processing pipeline is shown in bottom-up order in the lists box. That is, the data source is always the last item and modifiers are executed from the bottom to the top. The order of the modifiers in the processing pipeline can be changed with the arrow buttons to the right of the listbox. The delete button completely removes the selected modifier from the processing pipeline. The tool button with the light bulb lets you temporarily deactivate the selected modifier.

Tip

Double-clicking an entry in the listbox also activates/deactivates the entry.

4.4. Rendering

Rendering is the process of generating a two-dimensional image of the current atomic structure as seen through one of the viewports. The resulting image can be saved to an image file in various formats and be used for publication.

All rendering functions are found in Render tab of the command panel. This tab is labeled with the icon. Here, you find the Render Settings panel, which allows you to specify general settings. It is followed by the parameters panel of the selected renderer (see below). You can start the rendering process by pressing the Render Active Viewport button. OVITO will always use the viewing direction of the active viewport for rendering. The active viewport can be set by righ-clicking into one of the viewports.

OVITO supports different rendering backends (renderers) that produce the final image of the scene. They are integrated into the program as plug-ins to allow for easy addition of more renderers in the future. In the current version, OVITO provides two renderer backends:

Built-in OpenGL renderer

This is the default renderer. It is based on realtime rendering engine of OVITO, which uses OpenGL for displaying atoms. The OpenGL Renderer is optimized for fast operation and utilizes the available graphics hardware. The image quality is similar to the display in OVITO's realtime viewports.

POV-Ray renderer

POV-Ray is a third-party raytracing program that is freely available. It can produce high-quality pictures of geometric objects taking into account reflections, lighting, shadows and textures. The POV-Ray rendering plug-in of OVITO first translates the current scene including all the atoms into the format of POV-Ray. It then invokes the external POV-Ray program in the background and lets it render the image. After POV-Ray has finished, the resulting image is read back into OVITO. This all happens transparently for the user.

Note

This renderer is only available if you have built OVITO with the OVITO_BUILD_PLUGIN_POVRAY option enabled.
Tachyon renderer

Tachyon is a parallel ray tracing engine developed by John E. Stone and has been integrated into OVITO. Tachyon supports on-the-fly ambient occlusion lighting.

Note

This renderer is only available if you have built OVITO with the OVITO_BUILD_PLUGIN_TACHYON option enabled.

You can choose the renderer plug-in in the main menu under RenderSelect Renderer.

4.5. Exporting atomistic data

Sometimes it makes sense to re-export the atomistic data into a data file, which can be fed into the simulation program again. Another application of the export function is to store analysis results that have been calculated by an analysis modifier in OVITO. Or you can export the atomic positions to a POV-Ray file for further processing.

Choose FileExport from the main menu or press Ctrl+e. A dialog to select the destination filename and the file type will show up. Section 5.8 lists the available output formats.