Mesoscale microstructure simulations using the phase field method can be utilized to generate initial structures for large sacle molecular dynamics simulations. One application is the construction of nano-foam atomistic samples from simulations of spinodal decomposition.
MOOSE provides a built in system to template an atomic coordinate file in the
.xyz format from the simulation result in a given mesh file. The workflow is as follows
.xyzinput file with the desired underlying lattice and crystal structure
MOOSE will load the
.xyz input and finite element mesh superpose both and use thresholding to carve out rejected atoms while retaining accepted atoms. Finally a new
.xyz output is written containing only the accepted atoms, generating a porous microstructure.
SolutionRasterizer user object is derived from the
SolutionUserObject and inherits its input parameters. It takes the following additional input parameters:
||Output file containing the filtered (or mapped) atomic coordinate file.|
||Value of the selected non-linear variable to use in
The following input can be executed with the MOOSE Phase Field module executable and will
cis above a value of
[Mesh] type = GeneratedMesh dim = 3  [Problem] kernel_coverage_check = false solve = false  [Executioner] type = Steady  [UserObjects] [./soln] type = SolutionRasterizer system_variables = 'c' mesh = diffuse_out.e execute_on = timestep_begin variable = c xyz_input = in.xyz xyz_output = out.xyz # raster_mode = MAP raster_mode = FILTER threshold = 0.5 [../]