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Allow multiple meshes in project #2156

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endJunction merged 30 commits into ufz:master from endJunction:AllowMultipleMeshesInProject_j

Aug 23, 2018

Member

endJunction commented Jul 1, 2018

follow up of ctest fixes #2155

Main features are:

the addition of

   <meshes>
      <mesh>a.vtu</mesh>
      ...
   </meshes>

possibility (instead of a single mesh and geometry) to the project file.

Using the mesh names in non-uniform boundary conditions.

endJunction force-pushed the AllowMultipleMeshesInProject_j branch 4 times, most recently from 8a0e871 to a5cf05d Compare

July 5, 2018 11:02

endJunction added the WIP 🏗️ label

Member Author

endJunction commented Jul 5, 2018

I'm a little stuck with the parallelization part here. As soon as this is available, we can continue on the review...

endJunction force-pushed the AllowMultipleMeshesInProject_j branch 4 times, most recently from 3bdf44b to c5c2bc1 Compare

July 9, 2018 13:12

chleh reviewed

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chleh left a comment

So far it looks fine. Only minor comments.

Applications/ApplicationsLib/ProjectData.cpp Outdated

+                  auto optional_meshes = config.getConfigSubtreeOptional("meshes");
+                  if (optional_meshes)
+                  {
+                      DBUG("OK Reading multiple meshes.");

Collaborator

chleh Jul 9, 2018

Maybe drop OK.

Applications/ApplicationsLib/ProjectData.cpp Outdated

+                  if (optional_meshes)
+                  {
+                      DBUG("OK Reading multiple meshes.");
+                      for (auto mesh_config_line :

Collaborator

chleh Jul 9, 2018

Maybe only mesh_config.

Applications/ApplicationsLib/ProjectData.cpp Outdated

+                  {  // Read single mesh with geometry.
+                      WARN(
+                          "Consider switching from mesh and geometry input to multiple "
+                          "meshes input.");

Collaborator

chleh Jul 9, 2018

Here, pointing to some docu would be nice. TBD later? Add TODO?

Applications/ApplicationsLib/ProjectData.cpp Outdated

-                      auto pv =
-                          ProcessLib::ProcessVariable{var_config, _mesh_vec, _parameters};
+                      // Either the mesh name is given, or the first mesh's name will be
+                      // taken. Taking the first mesh's value is depricated.

Collaborator

chleh Jul 9, 2018

deprecated

Applications/ApplicationsLib/ProjectData.cpp Outdated

-                          ProcessLib::ProcessVariable{var_config, _mesh_vec, _parameters};
+                      // Either the mesh name is given, or the first mesh's name will be
+                      // taken. Taking the first mesh's value is depricated.
+                      std::string const mesh_name =

Collaborator

chleh Jul 9, 2018

There were times when you used to use auto much more often. ^^

ProcessLib/ProcessVariable.cpp Outdated

@@ @@ -30,6 +30,12 @@ MeshLib::Mesh const& findMeshInConfig( @@
                   //
                   std::string mesh_name;  // Either given directly in <mesh> or constructed
                                           // from <geometrical_set>_<geometry>.
+              #ifdef DOCUMENTATION

Collaborator

chleh Jul 9, 2018

Maybe rename the macro, e.g., OGS_THIS_IS_DOXYGEN_RUN.

...bles/process_variable/boundary_conditions/boundary_condition/Dirichlet/t_strict_bc_domain.md Outdated

+              example in LIE, where the displacement jump variable is defined only on the
+              fractures, or in case of hydro mechanics, where the pressure variable is defined
+              on lower order elements, the boundary mesh is not strictly required to coincide
+              with the part of the process variable's boundary part.

Collaborator

chleh Jul 9, 2018

Actually it's not checked if they coincide, but only if they have the same number of nodes, is it?

Member Author

endJunction Jul 13, 2018

It is assumed that geometrically the boundary mesh is fitting the bulk mesh. This is not checked, but "guaranteed" if the constructMeshesFromGeometries tool is used.
Now, if the strict_bc_domain is set, then all nodes of the bc_mesh for that variable must have a valid entry in the DOF table.

Collaborator

chleh Jul 17, 2018

That's what I wanted to say. 😄

And I'd add the following to the documentation:

It is assumed that geometrically the boundary mesh is fitting the bulk mesh.

ProcessLib/BoundaryCondition/NonuniformNeumannBoundaryCondition.cpp Outdated

@@ @@ -75,9 +75,17 @@ createNonuniformNeumannBoundaryCondition( @@
                                 mapping_to_bulk_nodes_property.c_str());
                   }
+                  auto const strict_bc_domain =

Collaborator

chleh Jul 9, 2018

can't that be moved to a central place for all BCs?

Documentation/Doxyfile.in Outdated

@@ @@ -2023,7 +2023,7 @@ INCLUDE_FILE_PATTERNS = @@
               # recursively expanded use the := operator instead of the = operator.
               # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-              PREDEFINED             =
+              PREDEFINED             = DOCUMENTATION

Collaborator

chleh Jul 9, 2018

Maybe rename the macro

Applications/FileIO/XmlIO/OpenGeoSysProject.xsd Outdated

@@ @@ -86,6 +86,21 @@ @@
                         </xs:complexType>
                       </xs:element>
                       <xs:element name="geometry" type="xs:string" minOccurs="0"/>
+                      <xs:element name="meshes" minOccurs="0">

Collaborator

chleh Jul 9, 2018

maxOccurs="1" or is that the default?

endJunction mentioned this pull request

Algorithms #2161

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wenqing reviewed

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wenqing left a comment

Looks good. Only small stuffs.

Documentation/ProjectFile/prj/meshes/mesh/a_axially_symmetric.md Outdated

		@@ -0,0 +1 @@
		\ogs_missing_documentation

Member

wenqing Jul 13, 2018

missing documentation.

NumLib/DOF/LocalToGlobalIndexMap.h Outdated

+                  /// The \c strict_bc_domain flag is controlling if the geometrical boundary
+                  /// domain and the domain of the global components (varaible_id,
+                  /// component_ids) must coincide. If set to false the not found global
+                  /// indices will not inserted into the derived DOF table.

Member

wenqing Jul 13, 2018

will not be

ProcessLib/BoundaryCondition/ConstraintDirichletBoundaryCondition.cpp Outdated

+                      config.getConfigParameter<bool>("strict_bc_domain", true);
+                  if (!strict_bc_domain)
+                  {
+                      DBUG("Allow non-strict bc domain and global component mapping.");

Member

wenqing Jul 13, 2018

bc --> BC?

ProcessLib/BoundaryCondition/GenericNaturalBoundaryCondition-impl.h

@@ @@ -45,6 +39,23 @@ GenericNaturalBoundaryCondition<BoundaryConditionData, @@
                           dof_table_bulk.getNumberOfVariableComponents(variable_id));
                   }
+                  if (_bc_mesh.getDimension() + 1 != global_dim)

Member

wenqing Jul 13, 2018

How about the case of a 3D mesh getting 1D BC?

Collaborator

chleh Jul 17, 2018

With out "ordinary" natural BCs a 1D BC for a 3D domain doesn't make sense, does it? For something like line sources the case is different, of course. But they don't fit our natural BCs anyway.

Member

wenqing Jul 17, 2018

I see that BCs on lines for 3D problem are excluded from this type of definition.

ProcessLib/BoundaryCondition/GenericNonuniformNaturalBoundaryCondition-impl.h

                   }
-                  if (_boundary_mesh->getDimension() + 1 != global_dim)
+                  if (_bc_mesh.getDimension() + 1 != global_dim)

Member

wenqing Jul 13, 2018

The same question.

ProcessLib/BoundaryCondition/NeumannBoundaryCondition.cpp Outdated

+                      config.getConfigParameter<bool>("strict_bc_domain", true);
+                  if (!strict_bc_domain)
+                  {
+                      DBUG("Allow non-strict bc domain and global component mapping.");

Member

wenqing Jul 13, 2018

bc-->BC?

ProcessLib/BoundaryCondition/NonuniformNeumannBoundaryCondition.cpp Outdated

-                  if (!boundary_mesh)
+                  // Surface mesh and bulk mesh must have equal axial symmetry flags!
+                  if (boundary_mesh.isAxiallySymmetric() != bulk_mesh.isAxiallySymmetric())

Member

wenqing Jul 13, 2018

I saw this twice. Is it possible to set it as a function?

ProcessLib/BoundaryCondition/NonuniformNeumannBoundaryConditionLocalAssembler.h Outdated

-                                                           n_and_weight.N, flux);
-                          _local_rhs.noalias() +=
-                              n_and_weight.N * (n_and_weight.weight * flux);
+                          // pos.setIntegrationPoint(ip);

Member

wenqing Jul 13, 2018

Is the comment needed?

endJunction force-pushed the AllowMultipleMeshesInProject_j branch 3 times, most recently from 0e05fd6 to 97eb96e Compare

July 18, 2018 16:46

endJunction force-pushed the AllowMultipleMeshesInProject_j branch 6 times, most recently from 8272cc3 to 52269b3 Compare

August 14, 2018 13:48

endJunction added 8 commits

August 22, 2018 17:18


          Pass domain mesh and meshes to PV construction.

fe17738


          [PL] PV: Parse mesh in the bc config.

7fb1015


          [PL] PV: Extract findMeshInConfig().

6a7e53c

Removing most of the code duplication in the BCs/STs creation.


          [PL] Pass bc mesh to boundary conditions.

648b15f


          [T] Update nonuniform BCs GWF tests.

781f625


          [T] LIE/M; Add geometries for fracture boundary.

8db8acf


          [T] CT; convert heterogeneous BCs ctest's meshes.

f3a0c7b

Rename bulk_node_ids and bulk_element_ids.
Use multiple meshes for setting the (heterogeneous) BCs.


          [doc] Add <meshes>/<mesh> tags descriptions.

37bc65d

endJunction added 11 commits

August 23, 2018 12:05


          [DE] Add <meshes/mesh> reading to XmlPrjInterface.

de07007


          [App/IO] Add meshes/mesh to OGSProject.xsd

cca9425


          [PL] BC; Consistent integration_points type.

74b4a91


          [MeL/IO] PETSc: Don't change mesh's name.

bfda662


          [T] EllipticPETSc; Use meshes in cube_1e3_neumann.

f993f1f


          [App/XmlIO] Extract meshType in project xsd.

0679de7


          [App/XmlIO] Add/update mesh in PV/BCs.

93a6f93


          [MGTL] Extract meshNameFromGeometry(geo_set, geo).

9b83db5

Used in construction of mesh names in two places.
This unifies the name.


          [PL] PV: Use findElementOrError() for mesh search.

f1c1090


          [PL] BC; Capital-case writing of BC.

898b064


          partitioned boundary meshes

aeeb28b

endJunction force-pushed the AllowMultipleMeshesInProject_j branch from f56ea8a to 0624ba8 Compare

August 23, 2018 10:19

endJunction added 3 commits

August 23, 2018 14:12


          [PL] BCs; In parallel setup BC might be empty.

492236d


          [T] Petsc/Neumann; Partition BC meshes.

3f221d2


          [T] GWF: parallelized square_1e1_neumann test.

77a47ef

endJunction force-pushed the AllowMultipleMeshesInProject_j branch from 0624ba8 to 796ccf3 Compare

August 23, 2018 12:13

endJunction added 6 commits

August 23, 2018 14:44


          [MeL] Add isBaseNode predicate.

b9712c9


          [NL] DOF; Test only base nodes for matching domain

89a6780


          [NL] DOF; Fix fct arg name in header.

fb13da3


          [PL] GWF; Fix ctest file name for vtkdiff cmp.

e8d9ffa


          [PL] BC; Move up axial symm. check.

e70210a


          [doc] Add axial symmetry attribute description.

e894e5c

endJunction force-pushed the AllowMultipleMeshesInProject_j branch from 796ccf3 to e894e5c Compare

August 23, 2018 12:44


          [T] LIE/HM; Fix p and disp_jump bc geometries.

b1ae94c

endJunction force-pushed the AllowMultipleMeshesInProject_j branch from 37f0ae6 to b1ae94c Compare

August 23, 2018 14:06

endJunction removed the WIP 🏗️ label

wenqing approved these changes

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wenqing left a comment

👍

endJunction merged commit d9eed42 into ufz:master

endJunction deleted the AllowMultipleMeshesInProject_j branch

August 23, 2018 16:17

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ogsbot commented Jun 19, 2020

OpenGeoSys development has been moved to GitLab.

See this pull request on GitLab.

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