Mesh Doctor

mesh-doctor is a python executable that can be used through the command line to perform various checks, validations, and tiny fixes to the vtk mesh that are meant to be used in geos. mesh-doctor is organized as a collection of modules with their dedicated sets of options. The current page will introduce those modules, but the details and all the arguments can be retrieved by using the --help option for each module.

Prerequisites

To use mesh-doctor, you first need to have installed the geos-mesh package using the following command:

python -m pip install --upgrade ./geos-mesh

Once done, you can call mesh-doctor in your command line as presented in the rest of this documentation.

Modules

To list all the modules available through mesh-doctor, you can simply use the --help option, which will list all available modules as well as a quick summary.

$ mesh-doctor --help
usage: mesh_doctor.py [-h] [-v] [-q] -i VTK_MESH_FILE
                {collocated_nodes,element_volumes,fix_elements_orderings,generate_cube,generate_fractures,generate_global_ids,non_conformal,self_intersecting_elements,supported_elements}
                ...
Inspects meshes for GEOSX.
positional arguments:
{collocated_nodes,element_volumes,fix_elements_orderings,generate_cube,generate_fractures,generate_global_ids,non_conformal,self_intersecting_elements,supported_elements}
      Modules
   collocated_nodes
      Checks if nodes are collocated.
   element_volumes
      Checks if the volumes of the elements are greater than "min".
   fix_elements_orderings
      Reorders the support nodes for the given cell types.
   generate_cube
      Generate a cube and its fields.
   generate_fractures
      Splits the mesh to generate the faults and fractures. [EXPERIMENTAL]
   generate_global_ids
      Adds globals ids for points and cells.
   non_conformal
      Detects non conformal elements. [EXPERIMENTAL]
   self_intersecting_elements
      Checks if the faces of the elements are self intersecting.
   supported_elements
      Check that all the elements of the mesh are supported by GEOSX.
options:
-h, --help
      show this help message and exit
-v    Use -v 'INFO', -vv for 'DEBUG'. Defaults to 'WARNING'.
-q    Use -q to reduce the verbosity of the output.
-i VTK_MESH_FILE, --vtk-input-file VTK_MESH_FILE
Note that checks are dynamically loaded.
An option may be missing because of an unloaded module.
Increase verbosity (-v, -vv) to get full information.

Then, if you are interested in a specific module, you can ask for its documentation using the mesh-doctor module_name --help pattern. For example

$ mesh-doctor collocated_nodes --help
usage: mesh_doctor.py collocated_nodes [-h] --tolerance TOLERANCE
options:
-h, --help              show this help message and exit
--tolerance TOLERANCE   [float]: The absolute distance between two nodes for them to be considered collocated.

mesh-doctor loads its module dynamically. If a module can’t be loaded, mesh-doctor will proceed and try to load other modules. If you see a message like

[1970-04-14 03:07:15,625][WARNING] Could not load module "collocated_nodes": No module named 'vtkmodules'

then most likely mesh-doctor could not load the collocated_nodes module, because the vtk python package was not found. Thereafter, the documentation for module collocated_nodes will not be displayed. You can solve this issue by installing the dependencies of mesh-doctor defined in its requirements.txt file (python -m pip install -r requirements.txt).

Here is a list and brief description of all the modules available.

`all_checks` and `main_checks`

mesh-doctor modules are called actions and they can be split into 2 different categories: check actions that will give you a feedback on a .vtu mesh that you would like to use in GEOS. operate actions that will either create a new mesh or modify an existing mesh.

all_checks aims at applying every single check action in one single command. The available list is of check is: collocated_nodes, element_volumes, non_conformal, self_intersecting_elements, supported_elements.

main_checks does only the fastest checks collocated_nodes, element_volumes and self_intersecting_elements that can quickly highlight some issues to deal with before investigating the other checks.

Both all_checks and main_checks have the same keywords and can be operated in the same way. The example below shows the case of all_checks, but it can be swapped for main_checks.

$ mesh-doctor all_checks --help
usage: mesh-doctor all_checks [-h] [--checks_to_perform CHECKS_TO_PERFORM] [--set_parameters SET_PARAMETERS]

options:
-h, --help            show this help message and exit
--checks_to_perform CHECKS_TO_PERFORM
                        Comma-separated list of mesh-doctor checks to perform.
                        If no input was given, all of the following checks will be executed by default: ['collocated_nodes', 'element_volumes', 'self_intersecting_elements'].
                        The available choices for checks are ['collocated_nodes', 'element_volumes', 'non_conformal', 'self_intersecting_elements', 'supported_elements'].
                        If you want to choose only certain of them, you can name them individually.
                        Example: --checks_to_perform collocated_nodes,element_volumes (default: )
--set_parameters SET_PARAMETERS
                        Comma-separated list of parameters to set for the checks (e.g., 'param_name:value'). These parameters override the defaults.
                        Default parameters are: For collocated_nodes: tolerance:0.0. For element_volumes: min_volume:0.0.
                        For non_conformal: angle_tolerance:10.0, point_tolerance:0.0, face_tolerance:0.0.
                        For self_intersecting_elements: min_distance:2.220446049250313e-16. For supported_elements: chunk_size:1, nproc:8.
                        Example: --set_parameters parameter_name:10.5,other_param:25 (default: )

`collocated_nodes`

Displays the neighboring nodes that are closer to each other than a prescribed threshold. It is not uncommon to define multiple nodes for the exact same position, which will typically be an issue for geos and should be fixed.

$ mesh-doctor collocated_nodes --help
usage: mesh_doctor.py collocated_nodes [-h] --tolerance TOLERANCE
options:
-h, --help              show this help message and exit
--tolerance TOLERANCE   [float]: The absolute distance between two nodes for them to be considered collocated.

`element_volumes`

Computes the volumes of all the cells and displays the ones that are below a prescribed threshold. Cells with negative volumes will typically be an issue for geos and should be fixed.

$ mesh-doctor element_volumes --help
usage: mesh_doctor.py element_volumes [-h] --min 0.0
options:
-h, --help              show this help message and exit
--min 0.0               [float]: The minimum acceptable volume. Defaults to 0.0.

`fix_elements_orderings`

It sometimes happens that an exported mesh does not abide by the vtk orderings. The fix_elements_orderings module can rearrange the nodes of given types of elements. This can be convenient if you cannot regenerate the mesh.

$ mesh-doctor fix_elements_orderings --help
usage: mesh_doctor.py fix_elements_orderings [-h] [--Hexahedron 1,6,5,4,7,0,2,3] [--Prism5 8,2,0,7,6,9,5,1,4,3]
                                             [--Prism6 11,2,8,10,5,0,9,7,6,1,4,3] [--Pyramid 3,4,0,2,1]
                                             [--Tetrahedron 2,0,3,1] [--Voxel 1,6,5,4,7,0,2,3]
                                             [--Wedge 3,5,4,0,2,1] --output OUTPUT [--data-mode binary, ascii]
options:
-h, --help              show this help message and exit
--Hexahedron 1,6,5,4,7,0,2,3
                        [list of integers]: node permutation for "Hexahedron".
--Prism5 8,2,0,7,6,9,5,1,4,3
                        [list of integers]: node permutation for "Prism5".
--Prism6 11,2,8,10,5,0,9,7,6,1,4,3
                        [list of integers]: node permutation for "Prism6".
--Pyramid 3,4,0,2,1     [list of integers]: node permutation for "Pyramid".
--Tetrahedron 2,0,3,1   [list of integers]: node permutation for "Tetrahedron".
--Voxel 1,6,5,4,7,0,2,3 [list of integers]: node permutation for "Voxel".
--Wedge 3,5,4,0,2,1     [list of integers]: node permutation for "Wedge".
--output OUTPUT         [string]: The vtk output file destination.
--data-mode binary, ascii
                        [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.

`generate_cube`

This module conveniently generates cubic meshes in vtk. It can also generate fields with simple values. This tool can also be useful to generate a trial mesh that will later be refined or customized.

$ mesh-doctor generate_cube --help
usage: mesh_doctor.py generate_cube [-h] [--x 0:1.5:3] [--y 0:5:10] [--z 0:1] [--nx 2:2] [--ny 1:1] [--nz 4]
                                    [--fields name:support:dim [name:support:dim ...]] [--cells] [--no-cells]
                                    [--points] [--no-points] --output OUTPUT [--data-mode binary, ascii]
options:
-h, --help              show this help message and exit
--x 0:1.5:3             [list of floats]: X coordinates of the points.
--y 0:5:10              [list of floats]: Y coordinates of the points.
--z 0:1                 [list of floats]: Z coordinates of the points.
--nx 2:2                [list of integers]: Number of elements in the X direction.
--ny 1:1                [list of integers]: Number of elements in the Y direction.
--nz 4                  [list of integers]: Number of elements in the Z direction.
--fields name:support:dim
                        [name:support:dim ...]: Create fields on CELLS or POINTS, with given dimension (typically 1 or 3).
--cells                 [bool]: Generate global ids for cells. Defaults to true.
--no-cells              [bool]: Don't generate global ids for cells.
--points                [bool]: Generate global ids for points. Defaults to true.
--no-points             [bool]: Don't generate global ids for points.
--output OUTPUT         [string]: The vtk output file destination.
--data-mode binary, ascii
                        [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.

`generate_fractures`

For a conformal fracture to be defined in a mesh, geos requires the mesh to be split at the faces where the fracture gets across the mesh. The generate_fractures module will split the mesh and generate the multi-block vtk files.

$ mesh-doctor generate_fractures --help
usage: mesh_doctor.py generate_fractures [-h] --policy field, internal_surfaces [--name NAME] [--values VALUES] --output OUTPUT
                                         [--data-mode binary, ascii] [--fractures_output_dir FRACTURES_OUTPUT_DIR]
options:
-h, --help              show this help message and exit
--policy field, internal_surfaces
                        [string]: The criterion to define the surfaces that will be changed into fracture zones. Possible values are "field, internal_surfaces"
--name NAME             [string]: If the "field" policy is selected, defines which field will be considered to define the fractures.
                        If the "internal_surfaces" policy is selected, defines the name of the attribute will be considered to identify the fractures.
--values VALUES         [list of comma separated integers]: If the "field" policy is selected, which changes of the field will be considered as a fracture.
                        If the "internal_surfaces" policy is selected, list of the fracture attributes.
                        You can create multiple fractures by separating the values with ':' like shown in this example.
                        --values 10,12:13,14,16,18:22 will create 3 fractures identified respectively with the values (10,12), (13,14,16,18) and (22).
                        If no ':' is found, all values specified will be assumed to create only 1 single fracture.
--output OUTPUT         [string]: The vtk output file destination.
--data-mode binary, ascii
                        [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.
--fractures_output_dir FRACTURES_OUTPUT_DIR
                        [string]: The output directory for the fractures meshes that will be generated from the mesh.
--fractures_data_mode FRACTURES_DATA_MODE
                        [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.

`generate_global_ids`

When running geos in parallel, global ids can be used to refer to data across multiple ranks. The generate_global_ids can generate global ids for the imported vtk mesh.

$ mesh-doctor generate_global_ids --help
usage: mesh_doctor.py generate_global_ids [-h] [--cells] [--no-cells] [--points] [--no-points] --output OUTPUT
                                          [--data-mode binary, ascii]
options:
-h, --help              show this help message and exit
--cells                 [bool]: Generate global ids for cells. Defaults to true.
--no-cells              [bool]: Don't generate global ids for cells.
--points                [bool]: Generate global ids for points. Defaults to true.
--no-points             [bool]: Don't generate global ids for points.
--output OUTPUT         [string]: The vtk output file destination.
--data-mode binary, ascii
                        [string]: For ".vtu" output format, the data mode can be binary or ascii. Defaults to binary.

`non_conformal`

This module will detect elements which are close enough (there’s a user defined threshold) but which are not in front of each other (another threshold can be defined). Close enough can be defined in terms or proximity of the nodes and faces of the elements. The angle between two faces can also be precribed. This module can be a bit time consuming.

$ mesh-doctor non_conformal --help
usage: mesh_doctor.py non_conformal [-h] [--angle_tolerance 10.0] [--point_tolerance POINT_TOLERANCE]
                                    [--face_tolerance FACE_TOLERANCE]
options:
-h, --help              show this help message and exit
--angle_tolerance 10.0  [float]: angle tolerance in degrees. Defaults to 10.0
--point_tolerance POINT_TOLERANCE
                        [float]: tolerance for two points to be considered collocated.
--face_tolerance FACE_TOLERANCE
                        [float]: tolerance for two faces to be considered "touching".

`self_intersecting_elements`

Some meshes can have cells that auto-intersect. This module will display the elements that have faces intersecting.

$ mesh-doctor self_intersecting_elements --help
usage: mesh_doctor.py self_intersecting_elements [-h] [--min 2.220446049250313e-16]
options:
-h, --help              show this help message and exit
--min 2.220446049250313e-16
                        [float]: The tolerance in the computation. Defaults to your machine precision 2.220446049250313e-16.

`supported_elements`

geos supports a specific set of elements. Let’s cite the standard elements like tetrahedra, wedges, pyramids or hexahedra. But also prismes up to 11 faces. geos also supports the generic VTK_POLYHEDRON/42 elements, which are converted on the fly into one of the elements just described.

The supported_elements check will validate that no unsupported element is included in the input mesh. It will also verify that the VTK_POLYHEDRON cells can effectively get converted into a supported type of element.

$ mesh-doctor supported_elements --help
usage: mesh_doctor.py supported_elements [-h] [--chunck_size 1] [--nproc 8]
options:
-h, --help              show this help message and exit
--chunck_size 1         [int]: Defaults chunk size for parallel processing to 1
--nproc 8               [int]: Number of threads used for parallel processing. Defaults to your CPU count 8.

Mesh Doctor

Prerequisites

Modules

all_checks and main_checks

collocated_nodes

element_volumes

fix_elements_orderings

generate_cube

generate_fractures

generate_global_ids

non_conformal

self_intersecting_elements

supported_elements