The first option under the General tab controls the size of the fonts used in the GUI when opening GeoDict (GUI Start-Up Font Size).

For example, increasing the GUI Start-Up Font Size results in the display of a larger font overall in the GUI.

GeoDict automatically stores a copy of the previous 3D structure, before applying any changes to it, until the Memory for Undo is filled up.

This allows to quickly undo any changes using the undo function.

The disadvantage of keeping a copy of the last structure is that some runtime and hard disk space is required for saving the structures. Thus, it can be disabled by setting the Memory for Undo to 0 MiB.

If Check for GeoDict Updates is checked, GeoDict will automatically search if updates are available (requires internet connection) and print a message if an update is found.

GeoDict will not automatically download or install those updates.

In the I/O (input/output) options panel, define how many days the log files should be kept. In the log files the events happening while running GeoDict are recorded, as well as debug outputs.

Also define whether the time a warning message is displayed should be limited, and the time of the limitation in seconds. After the entered time has passed, the message is closed automatically. If 0 is selected, pop-up messages are not shown at all.

In the Text Editor panel set which text editor will be opened automatically when editing macros and other editable files. Click Browse to search and set the path to the location where the executable for the favorite text editor is located.

For a list of text editor recommendations refer to the GeoPy Scripting handbook.

The last two options set the timeout options for floating license users only. Define after how many hours the Floater Release Timeout will be triggered. Then all non-required floaters are freed and are available for other users. This is especially useful if many long-running computations are performed. The same behavior occurs when pressing the Release Floaters button in the progress bar during a simulation run.

The Idle Timeout triggers if after the defined hours no computation or user interaction was made. Then all floaters, including the GeoDict-Base floater, are freed and available for other users. It is possible to re-acquire the freed floaters when returning to the GeoDict application in the then opening dialog.

In the GeoDict Thread Parallelization panel set the number of parallel processes (threads) GeoDict should use, e.g., for the visualization, for the image processing, and for the structure generation.

It is possible to set the Thread Mode to Max. Thread Number which equals the Number of CPUs the machine has. When not all available CPUs of the computer should be used, for example to allow other users to work simultaneously on the same machine or to improve the performance of other programs, the number of used parallel processes can be limited by setting a Manual Thread Number.

 

Choosing Automatic Thread Number uses the maximum number of cores, if up to eight cores are available. If more than eight cores are available, the maximum of eight and the number of available cores divided by two is used. For example, if the machine has 12 cores available, automatic thread number takes the maximum of 8 and 12/2=6 which is 8.

Check Run GeoDict solvers with low priority to make the system more responsive when working interactively while a GeoDict solver (e.g. LIR or SimpleFFT) is running.

For cluster computations, set the environment variable that holds the location of the node file, i.e., the file that contains the list of assigned compute nodes.

For MPI parallel computations, set the path to the MPI Installation that should be used for the parallelization. Select Automatic to look automatically for MPI installations.

For more information, refer to the High Performance Computing handbook.

A connected component is defined as a complete set of connected voxels with respect to the chosen neighborhood mode and component mode.

Checking Show Number of Connected Components or Show Number of Connected Components in 2D Slice, and clicking OK, adds the number of Components to the Statistics section in the Status section.

If the pore space is divided by the structure into several parts, it can be counted as one connected component with Count Pore Space as Single Component checked. The pore space does not count as an object and does not add to the number of Objects.

As an example, a simple periodic structure model containing 10 spheres is shown. At the corners, it is the same gray sphere that disappears and reappears on the other side. Two red spheres are also cut in half. They disappear and reappear in Z-direction. Three of the red spheres overlap and one of the red spheres touches a gray sphere.

The number of GAD Objects in 3D is 10, but the number of GAD Objects in 2D is only 4 (2 gray and 2 red spheres) in the 2D-Slice 126 in X-direction (shown below). The pore space is not counted as object.

Now, see how the connected components in 3D and 2D are counted when checking Show number of Connected Components and Show Number of Connected Components in 2D Slice.

Neighborhood Mode and Component Mode define criteria for the connectivity of the components and are explained below. For this example, we choose Face as Neighborhood Mode, which means that two voxels are connected if they share a face. As Component Mode we choose Pore / Solid, so that solid voxels can form a component independent of their Material ID.

The number of Objects 3D and 2D are the same as before. Connected components in the 2D slice shown above are 4 (1 gray sphere + 1 red sphere + 1 [1 red sphere+1 gray sphere] component + 1 pore space).

Connected components in 3D are 8 (3 gray spheres + 3 red spheres + 1 [3 red spheres+1 gray sphere] component + pore space).

The example structure shown is periodic, thus, objects that end on one side of the domain and reappear on the opposite side are counted as being the same connected component. Periodicity of the domain is saved in the structure file and can be edited through GadGeo → Edit Domain (see the GadGeo handbook for more information). This might change the number of components, e.g., if GAD objects lie outside of the domain that is non-periodic. When changing to a periodic domain the objects are then placed inside the domain and counted for the number of components.

The Neighborhood Mode defines if two voxels are connected (and belong, depending on the component mode, to the same connected component) or not. The different modes are explained using this example.

Two voxels can be connected through faces, edges, and corners. Voxels that share a face, do also share edges and corners, as you can observe for the red and the blue voxel. The blue and the green voxel share an edge and the corner points of this edge. Finally, the blue and the yellow voxel share only one corner point. This means, that voxels with common corners always belong to the same connected component.

Thus, checking Face is more restrictive than choosing Face or Edge, and this is more limiting than selecting Face, Edge or Corner.

When choosing the Neighborhood Mode Face only the red and the blue voxel are connected.

When choosing Face or Edge the red and the blue voxel and the blue and the green voxel are connected.

Finally, if Face, Edge or Corner is chosen, the red and the blue voxel, the blue and the green voxel and the blue and the yellow voxel are connected.

For structures with more than one material, selecting Pore / Solid from the Component Mode pull-down menu determines whether the components are considered connected or not, based on being empty voxels (background) or solid voxels (structure), regardless of their Material ID. When selecting Material ID, the Material ID of the voxels is determinant for the components to be considered connected or disconnected. In the following examples, the neighborhood mode is set to face.

• Setting the component mode to Pore /Solid in this example results in 4 connected components in 2D, as there are #1 (sphere), #2 (half red sphere top + half red sphere bottom), #3 (2 spheres touching), and #4 pore.

• Setting the component mode to Material ID leads to 6 connected components 2D, as there are #1 (gray sphere), #2 (half red sphere top + half red sphere bottom), #3 (red sphere), #4 (gray sphere), #5 (1 blue overlapping voxel), and #6 pore.