The main menu contains the following menu items:

Figure 5.1. The Render settings panel

This parameter panel lets you control the general settings used for rendering a static image or movie sequence of your scene.

To start the rendering process press the Render Active Viewport button above the Render Settings panel.

Figure 5.2. The Built-in OpenGL renderer settings panel

This renderer backend is the default built-in renderer used by OVITO to create static images of the current scene. It utilizes the same display engine as the realtime viewports.

Figure 5.3. The POV-Ray Renderer settings panel

This renderer backend is based on the external POV-Ray program. See Section 4.4 on how to activate this 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.

This renderer requires the external povray program to be installed on your system.

OVITO also has an export function that let's you export the scene to a file in the POV-Ray format. This allows you to further customize the POV-Ray scene before it is processed by the POV-Ray program.

This modifier performs an analysis based on the Ackland-Jones bond-angle distribution [Ackland and Jones, Phys. Rev. B 73, 054104 (2006)] to classify atoms w.r.t. to their local crystalline structure (FCC, BCC, HCP etc.).

The usage of this modifier is similar to the Common Neighbor Analysis modifier. See its documentation for details.

Figure 5.7. The parameter panel of the Add Expression Channel modifier

This modifier can be used to fill a data channel with new values based on a user-defined math expression. The mathematical formula specified by the user is evaluated by the modifier for every atom in the input structure an the results are stored in the selected target channel. The target data channel can be any existing or non-existing channel. This allows to control every atomic property (like position, color, etc.) with this modifier.

The mathematical expression can contain references to other atomic properties stored in the data channels of the input atoms objects. The list of input variables that may be used in the formula is derived from the available data channels and is displayed in the lower part of the modifier interface. Variable names are case-sensitive.

This modifier fills the Color channel according to the colors assigned to the atom types.

This modifier has no parameters.

This modifier assigns a color to all selected atoms. If no selection of atoms has been defined then the color is assigned to all atoms.

Note that selected atoms are usually shown in a special color (red) to indicate that they are selected. The selection color therefore masks the actual colors of the atoms (stored in the Color data channel). After applying this modifier the selection channel gets hidden, i.e. the selection color is no longer used to mark selected atoms. Instead you see the real colors of the atoms as they have been assigned by this modifier. But the selected atoms remain selected, i.e. you can apply additional modifiers that should operate on the same set of atoms.

Figure 5.8. The parameter panel of the Affine Transformation modifier

Applies an affine transformation to the atomic positions and/or the simulation cell. The transformation is specified as a 3 times 3 matrix plus a translation vector.

This modifier calculates the atomic displacement vectors. This is done by comparing two different configurations of the same system.

The current input file is considered as the current configuration of the system by the modifier. Additionally the user specifies a second input file (with the same number of atoms) which is taken as the reference configuration of the system. The modifier then calculates the displacement vectors by subtracting the reference position from the current position of each atom. The results are stored in the Displacement channel and can be visualized as arrows in the viewports. One can use the Color Coding modifier to visualize the displacements via colors.

In the parameter panel of this modifier you find a [Choose File...] button that lets you choose the input file containing the atomic reference positions. Please note that this input file has to contain exactly the same number of atoms as the current configuration of the system. This also means that you should not delete atoms from the system at an earlier point in the processing pipeline. For example a Slice modifier should always be placed after the Calculate Displacements modifier to ensure that the Calculate Displacements modifier sees all atoms contained in the input file which is fed into the processing pipeline. If the number of atoms do not match the Calculate Displacements modifier reports an error and the displacement vectors are not calculated at all.

A second point you should be aware of when using the Calculate Displacements modifier is the ordering of the atoms. Many parallel MD codes write the atoms in a random order to the output file and the ordering of atoms can change between time steps, especially in parallel simulations. To facilitate the tracking of individual atoms they therefore write a unique identifier (or index) for each atom into the output file. You have to make sure that this index is read from the atoms file during import into OVITO for both the current configurations as well as for the reference configuration to ensure the same ordering for both sets. Because if, for some reason, the ordering of the atoms is different in the two configurations compared by the Calculate Displacements modifier then you will most likely observe huge displacement vectors.

Below the parameter panel of the Calculate Displacements modifier your find a second panel that lets you configure the display parameters for the Displacement channel that is created by the modifier.

Figure 5.9. The parameter panel of the Color Coding modifier

This modifier colors all atoms based on a scalar property value of each atom. The Color coding modifier can be used to visualize a scalar and continuous property assigned to each atom, e.g. the atomic energy. The Color coding modifier operates as follows: The user first selects a data channel that should be used as source for the per-atom data values. For each atom the corresponding data value is scaled and clamped to the [0,1] range using the Start value and End value parameters of the modifier. This scaled value is then converted to a color based on the selected color gradient and then assigned to the atom.

The properties editor of the Color coding modifier provides two buttons that alter the start and end value parameters of the modifier: The Adjust range button sets the Start value and End value parameters to the minimum and maximum values found in the input data channel. This ensures that no clamping occurs during the color coding process. The Reverse range button swaps the Start value and End value parameters to reverse the color scale.

Figure 5.10. The parameter panel of the Common Neighbor Analysis modifier

This modifier performs a common neighbor analysis [Honeycutt and Andersen, J. Phys. Chem., 91, p. 4950] to classify atoms according to their local crystalline structure (FCC, BCC, HCP etc.). This analysis method is based on a nearest-neighbor graph, i.e. a mathematical graph consisting of edges that connect nearest neighbor atoms. Which atoms are considered nearest neighbors is determined by a user-defined cutoff distance. Atoms closer to each other than the given threshold radius are connected by an edge in the abstract graph. The common neighbor analysis (CNA) then exclusively operates on this mathematical graph structure, i.e. only the topological nearest-neighbor information is used to determine the crystalline arrangement around each atom. Each crystal structure exhibits a characteristic local topology of the nearest-neighbor graph.

A typical application of the CNA is to identify crystal defects in a crystalline solid.

The user has to specify a reasonable cutoff radius first. This decision depends on the primary crystal structure and the lattice constant of the material under consideration. To detect face-centered cubic (FCC) and hexagonal close packed (HCP) structures the cutoff radius must be chosen such that it lies midway between the first and the second shell of neighbor atoms. For body-centered cubic (BCC) and crystalline materials with a diamond structure the cutoff radius should, however, be chosen between the second and the third neighbor shell.

OVITO provides a database of optimal nearest-neighbor cutoff distances for many pure elements. These presets can be accessed via the drop-down list in the parameter panel. When building the nearest-neighbor graph the CNA modifer uses the periodicity settings of the simulation box. The periodic boundary conditions can be specified in the properties panel of the simulation box. To access the simulation box properties select the imported atoms file at the bottom of the modifier stack.

Note: To build the nearest-neighbor list of atoms for perodic systems, the analysis code applies the minimum image convention. This requires the simulation cell to be at least twice as wide as the cutoff radius in each spatial for which perodic boundary conditions are enabled. The analysis code detects when the simulation box is too small and will show an error message.

The Common Neighbor Analysis modifier is a so called analysis modifier. That means, in contrast to normal modifier, it analyzes the atomic dataset instead of modifying it. The analysis is computationally intensive and cannot be done in realtime, hence, the user has to explicitely press the Calculate button to run it. The analysis results, i.e. the local crystalline structure of each atom, get stored in the CNA Atom Type data channel of the atoms. In addition, a color is assigned to each atom that indicates its detected crystal structure. The color legend is located in the parameter panel of the modifier and colors can be changed by double-clicking on the entries of the legend.

A technical detail must be noted: The analysis is always performed on the current state of the atomic system as it is visible to the Common Neighbor Analysis modifier in the processing pipeline. If, for example, the Common Neighbor Analysis modifier is preceded by a Slice modifer that deletes some of the atoms then the CNA will assume that these atoms have never been there. The Common Neighbor Analysis modifier should therefore be placed very early in the processing pipeline to let it operate on the full system including all atoms. Normal modifiers like the Slice modifer should always be placed after the analysis modifiers.

This modifier simply deletes all atoms that are currently selected.

This modifier inverts the atom selection. All atoms that have not been selected previously will be selected by this modifier. All atoms that have been selected before will become unselected.

This modifier can be used to preserve a selection over time. Immediately after the modifier is applied to the atoms it records the current selection state of all atoms. From then on it will override any existing atom selection with its cached selection set, independent of animation time.

A typical application of this modifier is making the displacement or motion of atoms visible. You first use e.g. the Slice modifier to select a slab of atoms in a region you want to track. Then you apply the Freeze Selection modifier to freeze this selection for all times. Now you can jump to another timestep in your simulation and the initially selected atoms stay selected. You can easily see where they have moved to. Without the Freeze Selection modifier the Slice modifier would have been re-eavluated for the new timestep and the old selection would have got overwritten.

Note that the preserved selection state can only be sustained by the Freeze Selection modifier as long as the number of atoms does not change. In such a case the modifier will not restore the saved selection state but will leave the current selection state of the input atoms untouched.

This modifier selects all atoms of a specific type.

This modifier selects atoms based on a user-defined criterion. The user can specify a math expression that is evaluated for each atom to yield a boolean value. That is, if the math expression evaluates to exactly zero then the atom is not selected; otherwise it is selected.

The mathematical expression can contain variables that reference other atomic properties stored in the data channels of the input atoms objects. Therefore this modifier can be used to select atoms based on arbitrary properties like their position, atom type, energy etc. and any combination thereof. The list of input variables that are derived from the available data channels is displayed in the lower part of the modifier interface. Variable names are case-sensitive.

Copies all atoms and displaces them by the simulation cell vector to show the periodic images of the system.

This modifier can be used to check a simulation setup with periodic boundary conditions or to extend a small super cell. The display of the periodic images allows the user to quickly check whether a lattice, for instance, is properly continued on the other side of the simulation box.

Figure 5.11. The parameter panel of the Slice modifier

The Slice modifier cuts away atoms based on their position. There are two operation modes for the Slice modifier. It can either cut the set of atoms into two halfs and throw away one of them. Or it can cut out a thin slice from the atoms.

When the Slice modifier is selected in the modifier list then the slicing plane is visualized in the viewports. Its position is indicated by lines showing the plane's intersection with the simulation box. You should be aware that the slicing plane is going through the coordinate origin by default when you create a new Slicing modifier. If the simulation cell is located in some distance from the origin than it might not be intersected by the slicing plane and you won't see any indicators in the viewports. In this case try to vary the Distance parameter to make the plane intersect the simulation box.

At the bottom of the modifier's parameter panel you'll find several buttons that allow to align the slicing plane with the viewing direction of the selected viewport and vice versa. In addition you can align the slicing plane to a space plane defined by three non-coplanar atoms. To use this function first press the button and then pick three atoms in the viewports.

This modifier wraps around the atomic positions of all atoms that are outside of the simulation box. After this modifier has been applied all atoms are located inside the box.

Please note that the modifier acts only in those spatial directions for which periodic boundary conditions have been enabled. This is the case for all three directions of the simulation cell by default.

Stores the type of each atom. The definition of the atom types depends on the simulation software that produced the atom file. For example, the atom type could be encoded as the chemical element or as a plain number between 1 and the number of atom types in a simulation.

Internally, OVITO stores each atom's type as an integer starting with zero. It is used as an index into the array of atom types associated with the Atom Type data channel. Some of the entries in this list of atom types may be empty if there are no atoms of this type. For instance, the first atom type at index zerois undefined in most cases since most simulations programs start counting atom types at one. So there are no atoms with atom type zero and the Atom Type data channel contains only positive values.

The parameters of the Atom Type data channel control how the atom types are displayed in the viewports. This section of the manual is not complete yet.

Stores the atomic positions as absolute XYZ values. The units used for the atomic coordinates depend on the input file.

The Position data channel has several parameters that control the display of atoms in the viewports. This section of the manual is not complete yet.

Stores the displacement vector for each atom. The displacement vector specifies the motion of an atom between two states of the simulated system and can either be calculated using the Calculate displacements modifier or loaded from the input file if available.

The Displacement data channel has several parameters that control the display of displacement vectors in the viewports. This section of the manual is not complete yet.

Stores the local crystal structure as determined by the Common Neighbor Analysis modifier.

This section of the manual is not complete yet.

Stores the color of each atom. If the Color channel is present it overrides the colors specified in the Atom Type channel.

This section of the manual is not complete yet.

OVITO can import dump files written by the LAMMPS molecular dynamics package.

The import filter can parse dump files in text and binary format. Compressed files (with a .gz suffix) are decompressed on the fly.

OVITO can import data files written by the LAMMPS molecular dynamics package.

Only data files in the atomic format are supported. If the data files contains velocity vectors, they are imported.

Loading of compressed data files is supported. If the input file has a .gz suffix then it is decompressed on the fly.

OVITO can import XYZ text files written by several atomistic simulation packages. The XYZ format is a simple column-based format, which is documented here.

Loading of compressed files is supported. If the filename has a .gz suffix then it is decompressed on the fly.

OVITO can import POSCAR files written by the ab initio simulation package VASP.

OVITO can import files written by the molecular dynamics code IMD.

OVITO can write dump files as produced by the LAMMPS molecular dynamics package.

The export filter can write dump files in text and binary format.

If the output filename has a .gz suffix then the dump file is compressed on the fly.

OVITO can write data files, which can be read the LAMMPS molecular dynamics package.

If the atomic data to be exported contains velocity information it is written to the LAMMPS data file.

If the output filename has a .gz suffix then the data file is compressed on the fly.

OVITO can export the atomistic data to XYZ text files. The XYZ format is a simple column-based format, which is documented here.

OVITO can write POSCAR files as produced by the ab initio simulation package VASP.

OVITO can export the atomistic data to scene description files in the POV-Ray format. POV-Ray is a raytracing program.