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### Pipeline cloning

The Clone Pipeline function of OVITO lets you duplicate the currently selected data pipeline in order to visualize multiple datasets side by side or visualize the same dataset in several different ways. The function can be invoked by selecting Clone Pipeline from the pipeline menu depicted on the right.

The Clone Pipeline dialog will be displayed, letting you configure the cloning operation. Once you close the dialog by pressing Ok, the cloning operation is executed according to your settings as discussed below.

After the pipeline has been cloned, both the new copy and the existing data pipeline will be part of the current visualization scene and you will now see two objects in the viewports. The drop-down listbox at the top of the command panel's modification page indicates which of the pipelines is the currently selected one, allowing you to switch between the pipelines in the current scene. The modifiers of the currently selected pipeline are shown in the pipeline editor. You can also click on an object in the interactive viewports in order to select the pipeline associated with that object. The currently selected pipeline object is typically indicated by a white box color.

#### How pipeline cloning works

A pipeline in OVITO consists of a data source (typically an external data file feeding the pipeline) and a linear sequence of modifiers that have been inserted into the pipeline. In the user interface of OVITO the modifiers are typically laid out in a bottom-up fashion, with the data source at the bottom and the last modifier at the top. The data source delivers an input dataset (e.g. particles or other kinds of data objects), which is then processed by the modifiers one after the other. The end result leaving the pipeline is what gets displayed in the 3d viewports, i.e., a graphical rendering of the data object(s) appearing in the three-dimensional scene.

When cloning a pipeline, the data source and/or the modifiers of the original pipeline typically get copied over to the new pipeline. However, you can configure for each of these parts individually whether they should be duplicated or rather be shared by the original and the cloned pipeline. This gives you a great deal of flexibility: If you decide, for example, that the two pipelines should share the same data source, then both pipelines will always be fed with the same input dataset. If you subsequently pick a different input file for any one of the pipelines, this change will also affect the other pipeline as well. This synchronized mode can be useful, for example, to visualize the same input data in several different ways, typically by employing different modifiers in the two pipelines that share the same data source.

Another common use-case for OVITO'd pipeline cloning function is visualizing different input datasets side by side, always making sure that all modifier operations get applied in exactly the same way to both input datasets. In this case you would choose to duplicate the data source during the cloning operation and let the two pipelines share the modifiers instead. Then the pipelines will get fed with different input datasets, but it is ensured that each dataset will pass through the exact same sequence of modification steps.

For any data source or modifier of the existing pipeline, you can choose between four different cloning modes in the Clone Pipeline dialog:

Copy

  This will create an independent copy of the original object. Changing the object's parameters in either the original pipeline or the cloned pipeline will not affect the other pipeline.

Join

  The object will not be duplicated and the new pipeline will share the same object with the original pipeline. In fact, choosing this option results in a branched pipeline that starts at a single data source. Data flowing through the pipeline will be unique up to the branching point, i.e. the last modifier that was cloned using Join mode. Beyond the branching point, the two pipeline branches will be independent and can modify the data in different ways.

Share

  This cloning mode is only available for modifiers, not for the data source. It is a special variant of the Join mode providing some additional flexibility. The shared modifier becomes part of both pipelines and subsequently changing the modifier's parameter will affect both pipelines in the same way. However, the shared modifier can act on different data in the two pipelines, because unlike in a branched pipeline setup, which is always restricted to a single unique data source, the two pipelines can have different sources and/or modifiers preceding the shared modifier.

Skip

  This option simply leaves a modifier out in the cloned pipeline.

#### Further options

The location where the output data appears in the three-dimensional scene can be controlled independently for each pipeline. Typically you don't want the data of the cloned pipeline to appear in the same spatial location as the data of the original pipeline. This is why the Clone Pipeline dialog provides the option to displace the copied pipeline along the x, y or z-axis so that the copy appears side by side with the original pipeline in the scene.

Note that you can change the positioning of a pipeline object at any time using the Move and Rotate tools found in OVITO's toolbar. Using these tools you can still adjust the exact positioning of either the original or the cloned pipeline later on (see here for more information).

By default OVITO names each pipeline after the filename that serves as input for the pipeline. The two input fields at the bottom of the Clone Pipeline dialog allow you to override this default naming scheme and assign custom names to the original and/or the cloned pipeline, which can be very helpful to differentiate the two pipelines in the user interface, in particular if they share the same input file.

#### After cloning a pipeline

After cloning a pipeline, some modifiers or the data source may be shared between the original and the cloned pipeline. OVITO will indicate this in the user interface as we will see below.

For the following discussion, let us consider an example pipeline containing four modifiers, which are being cloned according to the following schematic picture:

The pipeline's data source and the first modifier (Cluster analysis) are reused in the cloned pipeline according to the selected mode Join. Thus, the two resulting pipelines will share the same upstream part. The Slice modifier is the first item for which a clone mode other than Join is selected. Thus, the cloned pipeline branches off before this modifier, which is being skipped in the cloned pipeline. Mode Copy has been selected for the Expression selection modifier. Accordingly, an independent copy of this modifier will be created and inserted into the cloned pipeline. This will enable you to change the selection expression in the second pipeline and select a different set of particles, for example. Finally, the Assign color modifier gets shared by both pipelines. That means the selected particles in both pipelines will always get assigned the same color.

After the cloning operation has been executed, you will see the newly created pipeline in the pipeline editor of OVITO:

The horizontal line labeled --Pipeline branch-- indicates that the part below the line is shared by the current pipeline with other pipelines in the same scene. Inserting, removing or changing modifiers below this line is thus going to affect also these other pipelines.

Some of the list entries in the pipeline editor are rendered using an italic font. OVITO uses the italic font to indicate that an object is shared between two or more pipelines. The Assign color modifier, for example, was cloned using mode Share. Thus, it is part of both the original pipeline and the cloned pipeline. Changing the color parameter of the Assign color modifier will thus trigger a recomputation of both pipelines in which the modifier is used.

You might realize later on that sharing the Assign color modifier was not a good idea. For instance, you may decide to assign a different color to the selected particles in the cloned pipeline but keep the color in the original pipeline. To do this, OVITO provides the function Replace with independent copy, which is marked with a red circle in the screenshot above. It allows you to replace the shared Assign color modifier with an independent copy. Subsequently, changing the parameters of the modifier will no longer affect the other pipeline.

Notice that also the visual elements are displayed using an italic font in the pipeline editor. This is because these visual elements are produced by the data source of the pipeline, which is located in the upstream section of the pipeline that is shared by multiple pipelines. Again, because these visual elements are shared objects, changing their parameters or turning their display on or off will affect the rendering of both datasets produced by the two pipelines. In this case you can also use the function Replace with independent copy to duplicate the visual elements if needed and control the visual appearance of particles and bonds individually for the original and the cloned pipeline.

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