Atoms currently supports only cloth in Maya, although it can be visualized and rendered in Houdini too.
The cloth cache files are generated in a post process and you will need a cache sequence file as input.
Please have a look at this tutorial to know more.
Cloth tools
Cloth setup
The Cloth Setup tool allows you to tag variation meshes as "hidden". You can access the tool via the Atoms menu: Atoms > Tools > Cloth > Cloth Setup
Hidden meshes will be added to your variations, but won't be rendered or displayed in the viewport by the Atoms Proxy.
They will only used when generating cloth caches, you would usually tag nRigid meshes as hidden if they are not meshes used at render time.
The Cloth Setup UI lets you tag, untag and select all hidden meshes.
Constraints
Currently only the "Component", "Component to Component" and "Point to Surface" constraints are supported.
Once you have created your nCloth setup in your variation scene, the variation builder will take care of exporting it alongside your variations.
Cloth Caches
There are two types of cloth caches: first and last. They both can be exported with the CFX simulation exporter.
Last: only the cloth cache will be applied to your mesh (no skinning)
First: when reconstructing the mesh, the mesh will have the cloth cache applied before the skinning (this value should not be used for cloth simulation).
A First cloth cache usually gets exported from a maya scene (i.e. a rig with some non-linear deformations that cannot be reproduced by blend shapes). Once you have an animated deformation you want to export, select the Maya group containing all the deforming geo and export the cloth cache with the CFX simulation exporter in Export mode. In the case of a rig, this process would happen with the rig in T pose.