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Insert Atoms

Group (Subgroup)

Synthetic Building (Packing)


This Filter creates a Vertex geometry where the Vertices represent atom positions. The Filter requires a Triangle surface mesh that bounds Features of different crystallographic orientation. The Filter then extracts the Triangles associated with each Feature and in parallel inserts atoms on the crystal lattice of each Feature. The steps associated with inserting the atoms in each Feature are as follows:

  1. Transform the coordinates of the Triangles into the reference frame of the Feature's crystallographic orientation using its stored orientation
  2. Determine the minimum and maximum X, Y and Z coordinate of the transformed Triangles
  3. Generate a grid of points starting at the minimum (X,Y,Z) coordinate using the lattice constants entered (with a||x, b||y and c||z) until reaching the maximum (X,Y,Z) coordinate. Add points at the proper positions given the crystal basis choosen by the user
  4. Transform list of points generated in 3 into the original Triangle reference frame using the inverse of the Feature's crystallographic orientation
  5. Check whether each point in the list falls inside of the n-sided polyhedron defined by the Triangles that bound the Feature. Remove the point from the list if it falls outside of the Feature's bounds. Assign the Feature's number to the point if it does fall inside of the Feature

After all Features have had atoms inserted, combine the point lists for all the Features.

Note: Since each Feature is treated independently (in parallel), the interface between neighboring Features may not be "in equilibrium". For example, at one point along the interface, each of the neighboring Features may have an atom fall just slightly outside its bounds. In this case, there may not be an atom on the "ideal" lattice for both Features, but maybe there should be a single atom that sits at the midpoint between the two ideal positions. The algorithm will instead just omit any atom from that area.


Name Type Description
Lattice Constants (Angstroms) float (x3) Lattice parameters (a, b, c) for the unit cell in Angstroms
Crystal Basis Enumeration Basis to be used when inserting atoms on lattice (currently Siple Cubic, Body-Centered Cubic and Face-Centered Cubic are available)

Required Geometry


Required Objects

Kind Default Name Type Component Dimensions Description
Face Attribute Array FaceLabels int32_t (2) Specifies which Features are on either side of each Face
Feature Attribute Array AvgQuats float (4) Specifies the average orientation of the Feature in quaternion representation

Created Objects

Kind Default Name Type Component Dimensions Description
Data Container VertexDataContainer N/A N/A Created synthetic volume Data Container name with Vertex Geometry
Attribute Matrix VertexData Vertex N/A Created Vertex Attribute Matrix name
Vertex Attribute Array AtomFeatureLabels int32_t (1) Specifies to which Feature each Vertex (or atom) belongs.

Example Pipelines

Please see the description file distributed with this Plugin

DREAM.3D Mailing Lists

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