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fix mesh/surface command

fix mesh/surface/planar command

Syntax:

fix ID group-ID mesh/surface file filename premesh_keywords premesh_values mesh_keywords mesh_values surface_keywords surface_values
fix ID group-ID mesh/surface/planar file filename premesh_keywords premesh_values mesh_keywords mesh_values surface_keywords surface_values

ID, is documented in fix command.
mesh/surface or mesh/surface/planar = style name of this fix command
file = obligatory keyword
filename = name of STL or VTK file containing the triangle mesh data
zero or more premesh_keywords/premesh_value pairs may be appended

premesh_keyword = type or precision or heal or verbose

  type value = atom type (material type) of the wall imported from the STL file
  precision value = length mesh nodes this far away at maximum will be recognized as identical (length units)
  heal value = auto_remove_duplicates or no
  verbose value = yes or no

zero or more mesh_keywords/mesh_value pairs may be appended

mesh_keyword = scale or move or rotate or element_exclusion_list temperature or mass_temperature

  scale value = factor
    factor = factor to scale the mesh in x-, y-, and z-direction (double value)
  move values = mx my mz
    mx my mz = move the mesh by this extent in x-, y-, and z-direction (length units)
  rotate values = axis ax ay az angle ang
    axis = obligatory keyword
    ax, ay, az = axis vector for rotation (length units)
    angle = obligatory keyword
  element_exclusion_list values = mode element_exlusion_file
    mode = read or write
    element_exlusion_file = name of file containing the elements to be excluded
  temperature value = T0
    T0 = Temperature of the wall (temperature units)
  mass_temperature value = mt0
    mt0 = mass (mass units) assumed for temperature update in the frame of surface sphere/heatable

zero or more surface_keywords/surface_value pairs may be appended

surface_keyword = surface_vel or surface_ang_vel or curvature or curvature_tolerant

  surface_vel values = vx vy vz
    vx vy vz = conveyor belt surface velocity  (velocity units)
  surface_ang_vel values = origin ox oy oz axis ax ay az omega om
    origin = mandatory keyword
    ox oy oz = origin of rotation (length units)
    axis = mandatory keyword
    ax ay az = axis vector for rotation (length units)
    omega = mandatory keyword
    om = rotaional velocity around specifyied axis (rad/time units)
  curvature value = c
    c = maximum angle between mesh faces belonging to the same surface (in degree) 
  curvature_tolerant value = ct
    ct = yes or no

Examples:

fix cad all mesh/surface file mesh.stl type 1

Description:

This fix allows the import of triangual surfeace mesh wall geometry for granular simulations from ASCII STL files or legacy ASCII VTK files. Style mesh/surface is a general surface mesh, and mesh/surface/planar represents a planar mesh. mesh/surface/planar requires the mesh to consist of only 1 planar face.

Generall, you can apply scaling, offset and rotation to the imported mesh via keywords scale, move, rotate. Operations are applied in the order as they are specified. The group-ID defines which particles will "see" the mesh, in case it is used as a granular wall.

One fix represents one wall with a specific material, where the material is identified via keyword type. If multiple meshes with different materials are desired, the respective meshes must be imported with different fix mesh/surface commands.

With the temperature keyword, you can define a constant temperature for a mesh in conjunction with heat conduction via fix heat/gran. Note that the actual calculation of the heat transfer happens only if you use the mesh in conjunction with a granular wall, see fix wall/gran.

With the optional surface_vel keyword, you can specify the imported mesh as conveyor belt. The velocity direction for each mesh face is given by the projection of the conveyor belt velocity parallel to the mesh face, the velocity magnitude for each mesh face is equal to the conveyor belt velocity. This ensures the model makes sense also in case the mesh is curved. Likewise, the optional rotation model activated via keyword surface_ang_vel mimics rotational motion of the mesh (e.g. for modeling a shear cell)

Quality checks / error and warning messages:

LIGGGHTS(R)-PUBLIC checks a couple of quality criteria upon loading a mesh. LIGGGHTS(R)-PUBLIC tries to give you as much information about the issue as possible.

Warning messages:

There should be no angle < 0.5 degrees in any element

All nodes should be within the simlation box

If any of the obove rules is not fulfilled, a warning is generated. Keyword verbose controls if details about the warning are written to the screen.

Error messages:

The curvature must not be larger than any angle in any mesh element

The number of neighbor elements must be <= 5 for any element

Mesh elements must not be duplicate

Coplanar mesh elements that share an edge must not overlap

Mesh elements must not leave the simulation domain

If any of the obove rules is not fulfilled, an error is generated and LIGGGHTS(R)-PUBLIC halts. Error messages are always verbose. If LIGGGHTS(R)-PUBLIC halts due to the last error, you might think about (a) changing the mesh import parameters (scale, move, rotate), (b) changing the mesh dynamics if a fix move/mesh is applied or using boundary m m m

There are a couple of features that help you read / repair a mesh which can not be read correctly in the first place:

precision

curvature

heal

element_exclusion_list

curvature_tolerant

The precision keyword specifies how far away mesh nodes can be at maximum to be recognized as identical. This is important for building the topology of the mesh and identify elements as neighbors. Normally, this should only be changed if the mesh file you are working with is suffering from precsion / round-off issues.

The curvature keyword lets you specify up to which angle between two triangles the triangles should be treated as belonging to the same surface (e.g. useful for bends). This angle is used to decide if (a) contact history is copied from one triangle to the other as the contact point proceeds and (b) if edge and corner interaction is calculated.

If LIGGGHTS(R)-PUBLIC stalls because of duplicate elements, you can try setting heal to auto_remove_duplicates. LIGGGHTS(R)-PUBLIC will then try to heal the geometry by removing duplicate elements.

With the optional element_exclusion_list keyword is used in mode 'write', LIGGGHTS(R)-PUBLIC will write a list of elements which have more than the allowed 5 face neighbors per surface element to a file. The 'read' mode can then use this file and will skip the elements in the list. However, you can also manually write such a file to exclude elements you do not want to have included

IMPORTANT NOTE: If you use the 'heal' or 'element_exclusion_list' keywords, you should check the changes to the geometry, e.g. by using a dump mesh/stl command.

The curvature_toleran keyword can simply turn off the check that the curvature must not be larger than any angle in any mesh element. This is typically not recommended, but can be used as a last resort measure.

Restart, fix_modify, output, run start/stop, minimize info:

This fix writes the STL data to binary restart files to be able to correctly resume the simulation in case the mesh is moved. None of the fix_modify options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions:

To date, only ASCII STL and VTK files can be read (binary is not supported). In the current implementation, each processor allocates memory for the whole geometry, which may lead to memory issues for very large geometries . It is not supported to use both the moving mesh and the conveyor belt feature.

Related commands:

fix wall/gran

Default: curvature = 0.256235 degrees, precision = 1e-8, verbose = no, heal = no