diff --git a/web/content/docs/tools/fileio/GMSH2OGS/index.md b/web/content/docs/tools/fileio/GMSH2OGS/index.md index 14634acfe80b43a3a124bca0bebbc33c83d99dcb..008f56348a88bd9813f3040af88243bfad746b2c 100644 --- a/web/content/docs/tools/fileio/GMSH2OGS/index.md +++ b/web/content/docs/tools/fileio/GMSH2OGS/index.md @@ -33,9 +33,10 @@ It also includes the outer boundary and inner boundary line elements. All files are stored in [Tests/Data/MeshLib/](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/MeshLib): - - the Gmsh generated mesh + +- the Gmsh generated mesh [A2-gmsh.msh](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/MeshLib/A2-gmsh.msh), - - and the corresponding result files +- and the corresponding result files [A2.vtu](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/MeshLib/A2.vtu), and the boundary meshes [A2_0.vtu](https://gitlab.opengeosys.org/ogs/ogs/-/blob/master/Tests/Data/MeshLib/A2_0.vtu) to @@ -50,18 +51,17 @@ and `-b` flags; the results are shown (z-translated) in the figure below. GMSH2OGS -i A2-gmsh.msh -o A2.vtu ``` - - Conversion without any additional flags yields a single VTU file with +- Conversion without any additional flags yields a single VTU file with outer and inner boundaries (line elements) included, shown in the very bottom. - - Adding only a `-e` flag results in a single VTU file, now without the line +- Adding only a `-e` flag results in a single VTU file, now without the line elements. - - Adding only a `-b` flag gives a single VTU file as in the first case *and* +- Adding only a `-b` flag gives a single VTU file as in the first case *and* additional eight files, each containing a line-element mesh corresponding to the physical groups; these are the white lines in the figure, shown again z-translated. - - Finally specifying both flags (`-e` and `-b`) produces a single VTU file +- Finally specifying both flags (`-e` and `-b`) produces a single VTU file without the line elements and additional eight boundary (subdomain) files.  - diff --git a/web/content/docs/tools/getting-started/video-tutorial/index.md b/web/content/docs/tools/getting-started/video-tutorial/index.md index e3cd07704a2865b87433f1fc17b6cdf1671b0f53..a93ca0ca685642198130ed2563671b9ef1a7cc8f 100644 --- a/web/content/docs/tools/getting-started/video-tutorial/index.md +++ b/web/content/docs/tools/getting-started/video-tutorial/index.md @@ -29,8 +29,7 @@ As a common programming language we use [Python](https://www.python.org). {{< youtube bkmubABAA_s >}} - -## Supplementary material: +## Supplementary material * [mesh_basin.msh](mesh_basin.msh) * [mesh_basin.py](mesh_basin.py) diff --git a/web/content/docs/tools/meshing-submeshes/constructMeshesFromGeometry/index.md b/web/content/docs/tools/meshing-submeshes/constructMeshesFromGeometry/index.md index f60503c30c8e22176e6734c0a7c6c57994cb25e0..d87272f1ba470046a8c0ad263d7da005283bec6d 100644 --- a/web/content/docs/tools/meshing-submeshes/constructMeshesFromGeometry/index.md +++ b/web/content/docs/tools/meshing-submeshes/constructMeshesFromGeometry/index.md @@ -52,5 +52,4 @@ yields new meshes for each named geometry: `single_fracture_3D_inlet.vtu`, `single_fracture_3D_top.vtu`, `single_fracture_3D_bottom.vtu`, and `single_fracture_3D_back.vtu`. - + diff --git a/web/content/docs/tools/meshing-submeshes/extract-boundary/index.md b/web/content/docs/tools/meshing-submeshes/extract-boundary/index.md index ad0bbe4b5783906fded1a8a1d88bca9197058947..dbe7721cec7e098338e24f3e0f72565f9802aa7e 100644 --- a/web/content/docs/tools/meshing-submeshes/extract-boundary/index.md +++ b/web/content/docs/tools/meshing-submeshes/extract-boundary/index.md @@ -38,14 +38,10 @@ and are required for flux calculations during a simulation run of OpenGeoSys. `ExtractBoundary -i square_1x1_quad.vtu -o square_1x1_quad_border.vtu` - + ### Extract the boundary from a tri mesh `ExtractBoundary -i square_1x1_tri.vtu -o square_1x1_tri_border.vtu` - + diff --git a/web/content/docs/tools/meshing-submeshes/extract-surface/index.md b/web/content/docs/tools/meshing-submeshes/extract-surface/index.md index 1ce4e3c7ae4f95ecae1a17a09fabaf1911c0e187..a170f4d0fa80ee14b767321be4a8a380695cf44d 100644 --- a/web/content/docs/tools/meshing-submeshes/extract-surface/index.md +++ b/web/content/docs/tools/meshing-submeshes/extract-surface/index.md @@ -39,7 +39,4 @@ Extracted top, bottom and side surfaces: - bottom `ExtractSurface -i Input.vtu -o BottomSurface.vtu -x 0 -y 0 -z 1` - side `ExtractSurface -i Input.vtu -o SideSurface.vtu -x 1 -y 1 -z 0 -a 45` - + diff --git a/web/content/docs/tools/meshing-submeshes/identifySubdomains/index.md b/web/content/docs/tools/meshing-submeshes/identifySubdomains/index.md index 6bdf6955589c5c922df7fbead3dab7652c6a4ab4..00e521df2bd6e02f0b0d9d3ecf8dfce1f4d7fbad 100644 --- a/web/content/docs/tools/meshing-submeshes/identifySubdomains/index.md +++ b/web/content/docs/tools/meshing-submeshes/identifySubdomains/index.md @@ -22,11 +22,9 @@ Given a "bulk" mesh (Tests/Data/Mechanics/Linear/disc_with_hole.vtu) and a quarter circle mesh for heterogeneous boundary condition. OGS requires two mappings into the "bulk" mesh, one for the nodes and one for the elements. - + -To create this mappings we run +To create these mappings we run ```bash identifySubdomains -m Tests/Data/Mechanics/Linear/disc_with_hole.vtu -s 1e-6 -o diff --git a/web/content/docs/tools/meshing/gmsh-interface/index.md b/web/content/docs/tools/meshing/gmsh-interface/index.md index ce6dcdc9a7ff4521e5fc7edaa12fe7d77018ee17..f1964c985545f5f8d1d144b49e6f7c350e659837 100644 --- a/web/content/docs/tools/meshing/gmsh-interface/index.md +++ b/web/content/docs/tools/meshing/gmsh-interface/index.md @@ -21,6 +21,7 @@ argument can be obtained with the `--help` option. ```bash geometryToGmshGeo --input <input file name> --output <output file> ``` + The `--input` argument is accepted multiple times. ## Simple examples @@ -28,11 +29,13 @@ The `--input` argument is accepted multiple times. ### First Example: Simple Geometry First, the Gmsh geometry file is create from the gml file [square_1x1.gml](square_1x1.gml): + ```bash geometryToGmshGeo -i square_1x1.gml -o /tmp/square_1x1.geo --mesh_density_scaling_at_points 0.05 ``` Then, the Gmsh geometry can be meshed: + ```bash gmsh /tmp/square_1x1.geo -2 -algo meshadapt -format msh22 -o /tmp/square_1x1.msh ``` @@ -45,9 +48,10 @@ gmsh /tmp/square_1x1.geo -2 -algo meshadapt -format msh22 -o /tmp/square_1x1.msh ### Second Example: Simple Geometry with Additional Geometrical Information First, the Gmsh geometry file is create from the gml files - - [square_1x1.gml](square_1x1.gml) - - [square_0.15_0.25x0.15_0.25.gml](square_0.15_0.25x0.15_0.25.gml) - - [square_0.45_0.55x0.45_0.55.gml](square_0.45_0.55x0.45_0.55.gml) + +- [square_1x1.gml](square_1x1.gml) +- [square_0.15_0.25x0.15_0.25.gml](square_0.15_0.25x0.15_0.25.gml) +- [square_0.45_0.55x0.45_0.55.gml](square_0.45_0.55x0.45_0.55.gml) ```bash geometryToGmshGeo -i square_1x1.gml @@ -57,6 +61,7 @@ geometryToGmshGeo -i square_1x1.gml ``` Then, the Gmsh geometry can be meshed: + ```bash gmsh /tmp/square_1x1.geo -2 -algo meshadapt -format msh22 -o /tmp/square_1x1.msh ``` diff --git a/web/content/docs/tools/meshing/remove-mesh-elements/index.md b/web/content/docs/tools/meshing/remove-mesh-elements/index.md index d50c3a997a8ea2f03b930cfd3dd368a3dfb49b6b..5f0c0d85a871858ecd5396cb7a9a03f10fe571e6 100644 --- a/web/content/docs/tools/meshing/remove-mesh-elements/index.md +++ b/web/content/docs/tools/meshing/remove-mesh-elements/index.md @@ -38,7 +38,7 @@ The corresponding element types differ from vtk cell types and can be found in M . It contains material ids 0 (red), 1 (yellow), 2 (turquoise) and 3 (blue).") - + ```bash removeMeshElements -i TestCube-ResetPropertiesInPolygonalRegion.vtu -o TestCube-removeMeshElements.vtu -n MaterialIDs --int-property-value 1 --int-property-value 2 --int-property-value 3 diff --git a/web/content/docs/tools/model-preparation/map-geometric-object-to-the-surface-of-a-mesh/index.md b/web/content/docs/tools/model-preparation/map-geometric-object-to-the-surface-of-a-mesh/index.md index 0983160fff3a69bfa4ef30b31c2ab240eaa96792..aa1c8f4e729d3e16610a9f2be4617fa99a093ba0 100644 --- a/web/content/docs/tools/model-preparation/map-geometric-object-to-the-surface-of-a-mesh/index.md +++ b/web/content/docs/tools/model-preparation/map-geometric-object-to-the-surface-of-a-mesh/index.md @@ -40,4 +40,5 @@ DOI:10.1007/s12665-013-2970-2 [download](http://link.springer.com/article/10.100 - [SubsurfaceMesh.vtu](SubsurfaceMesh.vtu) - [TestPolyline.gml](TestPolyline.gml) + </div> diff --git a/web/content/docs/tools/model-preparation/set-properties-in-polygonal-region/index.md b/web/content/docs/tools/model-preparation/set-properties-in-polygonal-region/index.md index 62ee62e1784e13d150a11eea29eb00fd38826161..b3f414b5b872d7e734f0b97133d5f881ebffb0fa 100644 --- a/web/content/docs/tools/model-preparation/set-properties-in-polygonal-region/index.md +++ b/web/content/docs/tools/model-preparation/set-properties-in-polygonal-region/index.md @@ -35,6 +35,7 @@ ResetPropertiesInPolygonalRegion --any_of -o [modified_mesh.vtu] ``` + By default all nodes of an element have to be inside the polygon to set the property on the element. By specifying the boolean switch `any_of` at the command line the criterion for element selection changes to 'at least one @@ -80,7 +81,7 @@ ResetPropertiesInPolygonalRegion -o hex_5x5x5_Region1-Layer1.vtu ``` -Here the elements with material ids 11 are displayed non-transparent. +Here the elements with the material ID of 11 are displayed non-transparent. The final mesh containing 12 material groups is represented in the right figure and was created by the command @@ -116,4 +117,5 @@ This workflow was successful used in the INFLUINS project cutting out the Unstru - [TestPolylines.gml](TestPolylines.gml) - [hex_5x5x5.vtu](hex_5x5x5.vtu) - [Regions.gml](Regions.gml) + </div> diff --git a/web/content/docs/tools/preprocessing/createIntermediateRasters/index.md b/web/content/docs/tools/preprocessing/createIntermediateRasters/index.md index fa7eb79a739b826b14b1e07599d6451ac6e32069..3db1d2e094e69051c80ebbe12baf8c051a3fb8af 100644 --- a/web/content/docs/tools/preprocessing/createIntermediateRasters/index.md +++ b/web/content/docs/tools/preprocessing/createIntermediateRasters/index.md @@ -55,7 +55,7 @@ createIntermediateRasters --file1 raster1.asc --file2 raster2.asc -o output.asc createIntermediateRasters --file1 raster1.asc --file2 raster2.asc -o output.asc -n 2 ``` - + ## Application diff --git a/web/content/docs/tools/workflows/Example-of-a-DGM-to-model-workflow/index.md b/web/content/docs/tools/workflows/Example-of-a-DGM-to-model-workflow/index.md index 400345ec3e7a891289f74fc34fc77e443fe4abc4..165a18aadc8536d80557bda2f0777d6f0fd9b94f 100644 --- a/web/content/docs/tools/workflows/Example-of-a-DGM-to-model-workflow/index.md +++ b/web/content/docs/tools/workflows/Example-of-a-DGM-to-model-workflow/index.md @@ -18,44 +18,44 @@ This part will prepare the DGM and bathymetry data as input for the model setup. ### Prepare elevation data -1. It is likely that you will need to download more than one remote sensing image when the study area is large or overlapping the borders of one section. Download the required DGM data (here `.tif` files) of the study area and load them into QGIS. +* It is likely that you will need to download more than one remote sensing image when the study area is large or overlapping the borders of one section. Download the required DGM data (here `.tif` files) of the study area and load them into QGIS.  -2. Merge the images with `Raster` -> `Miscellaneous` -> `Merge...`; select the `Input Layer`s. +* Merge the images with `Raster` -> `Miscellaneous` -> `Merge...`; select the `Input Layer`s.  -3. Extract a subregion of the (merged) DGMs and define the study area through a shape file. One may also use a predefined shape file and continue with step 5. Choose `New Shapefile Layer...` from the toolbar and enter a `File name` and a projection. +* Extract a subregion of the (merged) DGMs and define the study area through a shape file. One may also use a predefined shape file and continue with step 5. Choose `New Shapefile Layer...` from the toolbar and enter a `File name` and a projection.  -4. Edit the shape (`Toggle Editing` in toolbar), add points, and save the layer edits. +* Edit the shape (`Toggle Editing` in toolbar), add points, and save the layer edits.  -5. Clip the DGM with the shape file with `Raster` -> `Extraction` -> `Clip Raster by Mask Layer...`; define `Input Layer` and `Mask layer`, and assign the `Nodata value`. +* Clip the DGM with the shape file with `Raster` -> `Extraction` -> `Clip Raster by Mask Layer...`; define `Input Layer` and `Mask layer`, and assign the `Nodata value`.  -6. If the raster does not have the correct projection, you will have to reproject it with the appropriate target system with `Raster` -> `Projections` -> `Warp (Reproject)`; select the `Input Layer` and the `Target CRS`. +* If the raster does not have the correct projection, you will have to reproject it with the appropriate target system with `Raster` -> `Projections` -> `Warp (Reproject)`; select the `Input Layer` and the `Target CRS`.  -7. This example also includes bathymetry data, which was available as vector data (isoline in a shape file). This file must be reprojected to the same coordinate system as the raster before with `Vector` -> `Data Management Tools` -> `Reproject Layer`; select `Input Layer` and the `Target CRS`. +* This example also includes bathymetry data, which was available as vector data (isoline in a shape file). This file must be reprojected to the same coordinate system as the raster before with `Vector` -> `Data Management Tools` -> `Reproject Layer`; select `Input Layer` and the `Target CRS`.  -8. Before merging DGM and bathymetry, the shape data needs to be converted to raster data with `Raster` -> `Conversion` -> `Rasterize (Vector to Raster)`; define `Input Layer`, the z-value (`burn-in value`), the resolutions, and the `nodata value`. +* Before merging DGM and bathymetry, the shape data needs to be converted to raster data with `Raster` -> `Conversion` -> `Rasterize (Vector to Raster)`; define `Input Layer`, the z-value (`burn-in value`), the resolutions, and the `nodata value`.  -9. As bathymetry was given as "depth", this parameter needs to be converted to an "elevation"; use `Raster` -> `Raster Calculator` and define the `Output layer`, the `Output format` and the `Raster Calculator Expression` (shown formula only inverts the sign). +* As bathymetry was given as "depth", this parameter needs to be converted to an "elevation"; use `Raster` -> `Raster Calculator` and define the `Output layer`, the `Output format` and the `Raster Calculator Expression` (shown formula only inverts the sign).  -10. Merge the DGM and bathymetry rasters (as done in step 2), and save the merged file as a `.asc` file with `Raster` -> `Conversion` -> `Translate (Convert Format)`; define the `Input Layer` and the `Converted` output file. +* Merge the DGM and bathymetry rasters (as done in step 2), and save the merged file as a `.asc` file with `Raster` -> `Conversion` -> `Translate (Convert Format)`; define the `Input Layer` and the `Converted` output file.  ### Prepare study area features -11. To make the coastline part of the mesh, the merged DGM-bathymetry will be used to create a contour isoline at an elevation of `0.01 m` with `Extraction` -> `Contour...`; select the `Input Layer`, set the `Interval between contour lines` to a high value and set the `Offset from zero`. +* To make the coastline part of the mesh, the merged DGM-bathymetry will be used to create a contour isoline at an elevation of `0.01 m` with `Extraction` -> `Contour...`; select the `Input Layer`, set the `Interval between contour lines` to a high value and set the `Offset from zero`.  -12. If more than the `0.01 m` contour is present in the new shape file, remove the not required contours by right-clicking the new shape file and `Open Attribute Table`; click `Select features using an expression` and define the contours based on your liking that you want to exclude (here, anything with an elevation larger than 1 is removed). +* If more than the `0.01 m` contour is present in the new shape file, remove the not required contours by right-clicking the new shape file and `Open Attribute Table`; click `Select features using an expression` and define the contours based on your liking that you want to exclude (here, anything with an elevation larger than 1 is removed).  -13. Finish the selection (close attribute table) and remove the selected features by editing the shape (`Toggle Editing`) and clicking `Delete Selected`; save the changes. +* Finish the selection (close attribute table) and remove the selected features by editing the shape (`Toggle Editing`) and clicking `Delete Selected`; save the changes.  -14. The remaining features may be too highly resoluted (see red line in below figure); choose `Vector` -> `Geometry Tools` -> `Simplify...`, and select an `Input Layer` as well as the `Simplification method` with an appropriate `Tolerance`. +* The remaining features may be too highly resoluted (see red line in below figure); choose `Vector` -> `Geometry Tools` -> `Simplify...`, and select an `Input Layer` as well as the `Simplification method` with an appropriate `Tolerance`.  -15. Further, it might be useful to manually remove even more vertices from the polygon; `Toggle Editing` of the simplified shape and select and remove vertices. +* Further, it might be useful to manually remove even more vertices from the polygon; `Toggle Editing` of the simplified shape and select and remove vertices.  -16. The shape file used to clip the study area in step 5 will be used as the boundary of the model setup and be combined with the coastline. Firstly, convert the polygon of the study area to a polyline with `Vector` -> `Geometry Tools` -> `Polygons to Lines`; select the `Input Layer`. +* The shape file used to clip the study area in step 5 will be used as the boundary of the model setup and be combined with the coastline. Firstly, convert the polygon of the study area to a polyline with `Vector` -> `Geometry Tools` -> `Polygons to Lines`; select the `Input Layer`.  -17. Before merging the boundary and the coastline shapes, remove all fields from the boundary polyline through the `Attribute Table`; select everything and click `Delete field`. +* Before merging the boundary and the coastline shapes, remove all fields from the boundary polyline through the `Attribute Table`; select everything and click `Delete field`.  -18. Merge the boundary polyline and the coastline with `Vector` -> `Data Management Tools` -> `Merge Vector Layers`; select `Input Layers`. +* Merge the boundary polyline and the coastline with `Vector` -> `Data Management Tools` -> `Merge Vector Layers`; select `Input Layers`.  ## OGS model setup @@ -64,7 +64,7 @@ The next steps will use the OGS DataExplorer, GMSH, and ParaView to prepare the ### 3D Mesh creation -19. Load the merged boundary-coastline shape into the DataExplorer (`File` -> `Import` -> `Shape Files`). Creation of the 2D mesh can be done in two ways: +* Load the merged boundary-coastline shape into the DataExplorer (`File` -> `Import` -> `Shape Files`). Creation of the 2D mesh can be done in two ways: a) Either use GMSH: Save the geometry as a `.geo` file for usage in GMSH by choosing the tab `Geometry` and clicking the save icon. Afterwards, use GMSH to generate a 2D mesh to your liking and import it with `File` -> `Import Files` -> `GMSH files...`.  b) Or use the DataExplorer interface for GMSH: Use `Tools` -> `Create Mesh From Input Data...`. @@ -73,20 +73,20 @@ The next steps will use the OGS DataExplorer, GMSH, and ParaView to prepare the  Select the `Advanced` tab, choose `Adaptive meshing`, and remove the tick at `Delete GMSH geo-file after generating mesh` (in case you still want to manipulate the `.geo` file); click `OK`.  -20. To create a 3D mesh, the previously defined elevation data and subsurface layer data will be used to define multiple layers of the model. In the left-side tab `Meshes`, right-click the newly created (or imported) mesh, and choose `Edit mesh...` +* To create a 3D mesh, the previously defined elevation data and subsurface layer data will be used to define multiple layers of the model. In the left-side tab `Meshes`, right-click the newly created (or imported) mesh, and choose `Edit mesh...`  -21. In the new dialogue, `Specify the number of layers to add` (here 10), click `Add layers based on raster files`, and load all `.asc` files that define the different layers into the interface. Also, define a `Minimum thickness of layers` (here 5 height units). +* In the new dialogue, `Specify the number of layers to add` (here 10), click `Add layers based on raster files`, and load all `.asc` files that define the different layers into the interface. Also, define a `Minimum thickness of layers` (here 5 height units).  ### Boundary condition definition For the creation of the boundary conditions, use the following workflow. -22. Save the created 3D mesh as a `.vtu` file by selecting the 3D mesh in the `Meshes` tab and clicking the save icon. In the new dialogue, choose a output directory, filename, and the `Data mode`. +* Save the created 3D mesh as a `.vtu` file by selecting the 3D mesh in the `Meshes` tab and clicking the save icon. In the new dialogue, choose a output directory, filename, and the `Data mode`.  -23. To define water level and groundwater recharge, the top surface of the mesh will be used. Extract the surface with the tool [`ExtractSurface`]({{< ref "extract-surface" >}}). The following command is an example: +* To define water level and groundwater recharge, the top surface of the mesh will be used. Extract the surface with the tool [`ExtractSurface`]({{< ref "extract-surface" >}}). The following command is an example: `ExtractSurface -i SubsurfaceMesh.vtu -o exSurf.vtu -x 0 -y 0 -z -1 -a 30` -24. ParaView will be used to define boundary and initial condition values. +* ParaView will be used to define boundary and initial condition values. For boundary conditions, a separation of the water level (Dirichlet) and recharge (Neumann) boundary condition is required. Load the extracted top surface into ParaView and apply the following filter pipeline: a) Apply a `Calculator` with the operation `coordsZ` to get a new parameter field with elevation data. b) Apply a `Threshold` and define the value range from the lowest to the water level (here -35 to 0.01 height units); this will be the input file for the Dirichlet boundary condition. @@ -94,5 +94,5 @@ For boundary conditions, a separation of the water level (Dirichlet) and recharg d) repeat b) and c) on the `Calculator` from a) but with the value range water level to highest value (in the `Threshold`), and define the recharge value for the land area (in the `Calculator`). e) Save the "land" and "water" meshes as `.vtu` files.  -25. Define the `.prj` file of your setup, including the 3D mesh and boundary condition meshes and run the simulation. +* Define the `.prj` file of your setup, including the 3D mesh and boundary condition meshes and run the simulation.  diff --git a/web/content/docs/tools/workflows/create-a-simple-parallel-model/index.md b/web/content/docs/tools/workflows/create-a-simple-parallel-model/index.md index 7b717959751c9016651770ea5b00de16e5456494..c3990bc9fc4f6245df2b389f0e2222c55f0652c1 100644 --- a/web/content/docs/tools/workflows/create-a-simple-parallel-model/index.md +++ b/web/content/docs/tools/workflows/create-a-simple-parallel-model/index.md @@ -10,8 +10,8 @@ author = "Thomas Fischer" ## Unsupported Processes -So far, LIE related processes are not supported to use - the parallel FEM scheme with PETSc. +So far, LIE related processes are not supported to use +the parallel FEM scheme with PETSc. ## Software Modules and Compilation on EVE