Exporting Surface Mesh Data

OVITO
1

Hi,

I am quite new to OVITO and I face a problem while exporting surface mesh data. I am using OVITO v3.12.2 the basic GUI version.

What I look for might be part of OVITO Pro already but anyways I am adding some details to my post just in case you might require it. I am uploading bunch of data and applying modifiers before I create the surface mesh. Below I add a summary. The data I work on is a LAMMPS dump file.

  1. I read a LAMMPS dump file that contains the trajectories of the particles Specifically;
    id - mol - type - x - y - z - ix - iy - iz - vx - vy - vz
  2. Then I read another dump file that contains the bond data using the load trajectory modifier. The dump file looks like this.
    particle id1 - particle id2 - bond type
    Of course dump files include necessary headers generated by LAMMPS.
  3. I replicate the simulation domain into positive and negative z direction by the replicate modifier.
  4. I apply the following expression selection : Position.X < 50 || Position.X > 140 || Position.Y > 10 || Position.Z < 0 || Position.Z > 30.
  5. I delete the selected.
  6. I use the cluster analysis modifer based upon the bonds.
    7,8) I apply this expression selection; Cluster > 10 and delete selected.

At the final stage I create a surface mesh using the construct surface mesh modifier with probe radius 0.5 and a smoothing level of 4. I then transfer particle properties to surface. This modifer creates a surfaces tab where I can see the coordinates of the nodal points of the surface triangulation and the cluster they belong. Now if I know which triangle belongs to what cluster I can calculate the surface area of the aggregates and/or calculate the volume enclosed by the surface. However I cannot export this data appering under the surfaces tab. Is there a way to export this using the GUI? Should I switch to API? Is it already part of OVITO Pro?

Thanks in advance.

2

Hi,

You cannot export mesh properties directly from the GUI. By default, meshes can only be exported in VTK format.

However, in the Python API, you can freely access all mesh properties as NumPy arrays.

OVITO Pro includes an extension that allows the export of surface meshes, including all their properties, as NumPy .npz files. These properties can be accessed in a dictionary-like manner. This extension could be adapted to export the data in a human-readable ASCII format if needed.