fix mesh/surface command — LIGGGHTS v3.X documentation

# fix mesh/surface command

# fix mesh/surface/planar command

## Syntax

    fix ID group-ID mesh/surface data_keyword data_value premesh_keywords premesh_values mesh_keywords mesh_values surface_keywords surface_values
    fix ID group-ID mesh/surface/module_list data_keyword data_value premesh_keywords premesh_values mesh_keywords mesh_values surface_keywords surface_values module_keywords module_values
    fix ID group-ID mesh/surface/planar data_keyword data_value 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
- module_list = list of mesh modules separated by /
- one data_keyword/data_value pair needs to be appended
- data_keyword = file or fix

    file value = name of STL or VTK file containing the triangle mesh data
    fix value = id of a fix that can generate meshes (e.g. this one using the extrude_planar keyword)

- zero or more premesh_keywords/premesh_value pairs may be appended
- premesh_keyword = type or precision or heal or min_feature_length or element_exclusion_list or verbose

    type value = atom type (material type) of the wall imported from the STL file
    region value = ID of region to filter elements which are imported
    precision value = length mesh nodes this far away at maximum will be recognized as identical (length units)
    heal value = auto_remove_duplicates or no
    min_feature_length value = exclude element if belongs to an entity where no element is larger than this (length units)
    element_exclusion_list values = mode element_exlusion_file
      mode = read or write
      element_exlusion_file = name of file containing the elements to be excluded
    verbose value = yes or no

- zero or more mesh_keywords/mesh_value pairs may be appended

    mesh_keyword = scale or move or rotate or temperature or mass_temperature or extrude_planar:l
      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
        ang = rotation angle (degrees)
      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
      extrude_planar value = length
        length = length (length units) that a planar mesh is extruded in anti-normal direction

- 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 = rotational 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

- zero or more module_keywords/module_value pairs may be appended if a mesh module is used

    see the respective mesh module parameter list for details

## Examples

    fix cad all mesh/surface file mesh.stl type 1
    fix cad1 all mesh/surface/stress/deform file meshes/plate.stl type 1 scale 1.0 wear finnie
    fix extrude all mesh/surface file plane.stl type 1 extrude_planar 0.1
    fix side_walls all mesh/surface fix extrude type 1

## Description

This fix allows the import of triangular surface 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.

The region keyword can be used to filter the elements which are imported. An element is only imported if all of its vertices is inside the specified region. Please note that the geometric extent of this region refer to the unscaled, unmoved, and unrotated original state of the geometry.

In general, 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 rotation via rotate is performed around the rotation axis that goes through the origin (0,0,0) and in the direction of axis.

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.

The extrude_planar option allows to extrude a planar mesh in direction of the anti-normal by a specified length values. After a run 0 command this fix will hold the generated triangles which can be used in another mesh/surface fix that uses the fix instead of file keyword.

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)

Mesh modules:

The “mesh/surface” fix allows for several mesh modules to be appended. A complete list of the available mesh modules can be found in Section mesh modules.

Note that some of these modules are dependent on each other and some are mutually exclusive. The order of the mesh modules is important and the arguments for each mesh module need to be appended in the same order as the modules.

Warning

When using the deform, heattransfer or liquidtransfer module and periodic boundary conditions the mesh needs to fulfill the following properties: (i) a triangle is not allowed to be in contact with itself through periodic boundaries, (ii) if two triangles are in contact inside the domain, they are not allowed to be in contact through periodic boundaries. Note that these restrictions are not validated by LIGGGHTS(R)-PUBLIC and must be ensured by the user.

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 (soft limit for angles)
- All nodes should be within the simulation box

If any of the above 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
- There must be no element with an angle < 0.0181185 degrees in any element (hard limit for angles)
- 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 (based on the center of the element)

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
- min_feature_length
- 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
- have an angle below 0.0181185 degrees
- are duplicate

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

Warning

The element_exclusion_list write model works in serial only. However, this is not a real restriction, since you can generate the exclusion lists in serial, but then read them to import the mesh into a parallel simulation

Warning

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.

With the min_feature_length option, you can exlude elements which do not belong to an entity which has any element larger than min_feature_length. In this context, ‘entity’ is defined by the ‘neighborhood’ of the element. min_feature_length also writes to the exclusion list, and can thus only be used along with the ‘element_exclusion_list’ feature. This feature is only available in the PREMIUM version of LIGGGHTS.

The curvature_tolerant 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 directly. However, some mesh modules do have fix_modify options, please refer to the respective module for further information.

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