[Paraview] Molecular dynamics from lammps

[Berk Geveci]

Dear Oksana,

You do need to generate a volumetric mesh first and then slice it to
generate a polygonal mesh. The volumetric mesh needs to interpolate your
values in space somehow. This is what Delaunay would give you - it will
generate a mesh where each atom is a node of a tetrahedra and the values
are interpolated over the tets. Is the interpolation the cause of "which do
not represent my structure properly"? What do you expect the slice to look
like? Maybe you need to project the closest atoms to the slice instead of
interpolating?

Best,
-berk

On Tue, Jul 7, 2015 at 10:39 AM, Oksana <oksana_golovnya at mail.ru> wrote:

> Dear community,
>
> I am trying to visualize array of atoms with their displacement vectors in
> Paraview. The structure is complicated and cannot be represented by
> StructuredGrid. The goal is to have slices with surface vectors
> (displacement) and atoms. I have tried two ways:
>
> 1.       Generate a vtk file. In this case I have a polydata of points
> and vectors, but I cannot use SurfaceVectors filter in this dataset. I
> tried Delaunay3D filter to produce a grid, but it produces too many cells,
> which do not represent my structure properly, and instead of one vector per
> atom I have some strange distribution.
>
> 2.       Load lammps dump file. In this case after MergeBlocks and
> Calculator filters I have unstructured grid with points and vectors, but
> cannot use this vectors in Slice->SurfaceVector pipeline anyway.
> SurfaceVectors are inactive.
>
> I understand that in the first case I need to generate a grid with each
> atom inside one cell. However, I do not know how to do it. And in the
> second I do not understand why SurfaceVectors are inactive on the
> unstructured grid? I would appreciate any help, explanation or reference
> how to do it right.
>
> Thanks.
>
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