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Expand Up @@ -18,14 +18,14 @@ The modifier can be found under the label "Denoise particle positions" in the OV

## Parameters

| GUI label | Python name | Description |
|----------------------------------|--------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **Number of denoising steps** | `steps` | Number of denoising iterations taken. More iterations require more time. You can check the mean displacement per iteration graph to assess convergence. |
| **Nearest neighbor distance** | `scale` | Estimation of the nearest neighbor distance used to scale the coordinates before they are input into the model. If this is `None`, OVITO will try to estimate the correct nearest neighbor distance. |
| **Crystal structure / material system** | `structure` | Allows you to select one of: "FCC", "BCC", "HCP", or "SiO2", depending on your input structure. Note that an SiO2 structure requires a type named "Si" and "O". If you don't want to use any of the default material systems, you can select "Custom". In that case, OVITO will not estimate the "Nearest neighbor distance" and it has to be provided by the user. |
| **Model file path** | `model_path` | Allows you to define a custom PyTorch model. The model will be loaded from the path entered. If this is set to `None`, the default models for "SiO2" or "Cu" shipped with [graphite](https://github.com/LLNL/graphite/) will be loaded. |
| **Device** | `device` | Allows you to select your computing device from: "cpu", "cuda", "mps". Only available devices will be shown. Please read the "Installation" section for additional information. |
| **Only selected** | `only_selected` | Apply the modifier only to the selected particles. Following the convention set by other modifiers, even atoms that are not selected will be used as neighbors. |
| GUI label | Python name | Description | Default |
|----------------------------------|--------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| --------|
| **Number of denoising steps** | `steps` | Number of denoising iterations taken. More iterations require more time. You can check the mean displacement per iteration graph to assess convergence. | `8` |
| **Nearest neighbor distance** | `scale` | Estimation of the nearest neighbor distance used to scale the coordinates before they are input into the model. If this is `None`, OVITO will try to estimate the correct nearest neighbor distance. | `None` |
| **Crystal structure / material system** | `structure` | Allows you to select one of: "FCC", "BCC", "HCP", or "SiO2", depending on your input structure. Note that an SiO2 structure requires a type named "Si" and "O". If you don't want to use any of the default material systems, you can select "Custom". In that case, OVITO will not estimate the "Nearest neighbor distance" and it has to be provided by the user. | `None` |
| **Model file path** | `model_path` | Allows you to define a custom PyTorch model. The model will be loaded from the path entered. If this is set to `None`, the default models for "SiO2" or "Cu" shipped with [graphite](https://github.com/LLNL/graphite/) will be loaded. | `None` |
| **Device** | `device` | Allows you to select your computing device from: "cpu", "cuda", "mps". Only available devices will be shown. Please read the "Installation" section for additional information. | `cpu` |
| **Only selected** | `only_selected` | Apply the modifier only to the selected particles. Following the convention set by other modifiers, even atoms that are not selected will be used as neighbors. | `False` |

## Example

Expand Down Expand Up @@ -73,4 +73,4 @@ Tested on (using conda):
- torch-geometric == 2.5.3

## Contact
Daniel Utt [email protected]
Daniel Utt [email protected]

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