dump meshedParticle command

Purpose

Dumps meshed representation of particles to files

Syntax

dump ID group-ID style N file mesh mesh-file optional_keywords optional_values

  • ID = user-assigned name for the dump

  • group-ID = ID of the group of atoms to be dumped

  • style = meshedParticle

  • N = dump every this many timesteps

  • file = name of file to write dump info to

  • mesh = mandatory keyword

  • mesh-file = path of a .stl used to represent particles

  • zero or more optional_keywords/optional_values pairs may be appended scale value = scaling factor used to scale the imported stl mesh data_file value = path to a text-file containing user-defined color values disable_color_output value = yes or no

Examples

dump meshedParticle all meshedParticle 100 post/particles*.vtk mesh cube.stl
dump dmp3 all meshedParticle 200 particles.vtk mesh cube.stl scale 4
dump dmp2 all meshedParticle 100 post/particles*.vtk mesh cube.stl data_file myData.txt

Description

meshedParticle dumps a meshed representation of the particles given by the mesh keyword argument. This mesh is moved and rotated to all of the particles positions. Each of the cells has a unique id called “color”. Color output can be disabled, however, by adding disable_color_output yes to the dump command.

Warning

If color output is enabled, this dump has a hard limit of #particles x #triangles < 16.7Mio

The keywords scale and data_file are optional. If the scale keyword is used, the mesh is scaled with the specified value. If no data_file is given, the dump automatically calculates a “color” value with the unique particle-ID and the number of cells of the mesh. If a data_file is present, the particle-ID and cell-ID of the mesh determine the index of the value from the data_file. If the $*data_file* has not enough data, the index is wrapped and a warning is displayed.

The data_file format is simply

value1
value2
value3
...

Dumps are performed on timesteps that are a multiple of N (including timestep 0) and on the last timestep of a minimization if the minimization converges. Note that this means a dump will not be performed on the initial timestep after the dump command is invoked, if the current timestep is not a multiple of N. This behavior can be changed via the dump_modify first command, which can also be useful if the dump command is invoked after a minimization ended on an arbitrary timestep. N can be changed between runs by using the dump_modify every command. The dump_modify every command also allows a variable to be used to determine the sequence of timesteps on which dump files are written. In this mode a dump on the first timestep of a run will also not be written unless the dump_modify first command is used.

The specified filename determines how the dump file(s) is written. The default is to write one large text file, which is opened when the dump command is invoked and closed when an undump command is used or when Aspherix® exits.

Dump filenames can contain one wildcard character. If a “*” character appears in the filename, then one file per snapshot is written and the “*” character is replaced with the timestep value. For example, tmp.dump.* becomes tmp.dump.0, tmp.dump.10000, tmp.dump.20000, etc. Note that the dump_modify pad command can be used to ensure all timestep numbers are the same length (e.g. 00010), which can make it easier to read a series of dump files in order with some post-processing tools.

Dump_modify:

This keyword can be influenced by several dump_modify options.

Restrictions

Only works with the atom_style superquadric.

Default

scale = 1