From 86b35a15d6bda1404836a4db233e4268e424b477 Mon Sep 17 00:00:00 2001
From: Thomas Fischer <thomas.fischer@ufz.de>
Date: Mon, 19 Apr 2021 12:35:36 +0200
Subject: [PATCH] [PL/Output] Distinguish between bulk and non-bulk meshes.
---
ProcessLib/Output/Output.cpp | 26 ++++++++--------
ProcessLib/Output/ProcessOutput.cpp | 47 +++++++++++++++++++++++++++++
ProcessLib/Output/ProcessOutput.h | 3 +-
3 files changed, 62 insertions(+), 14 deletions(-)
diff --git a/ProcessLib/Output/Output.cpp b/ProcessLib/Output/Output.cpp
index 8249b314ba9..4da2b755d66 100644
--- a/ProcessLib/Output/Output.cpp
+++ b/ProcessLib/Output/Output.cpp
@@ -284,7 +284,7 @@ void Output::doOutputAlways(Process const& process,
bool output_secondary_variable = true;
// Need to add variables of process to vtu even no output takes place.
addProcessDataToMesh(t, x, process_id, process.getMesh(), dof_tables,
- process.getProcessVariables(process_id),
+ dof_tables, process.getProcessVariables(process_id),
process.getSecondaryVariables(),
output_secondary_variable,
process.getIntegrationPointWriter(process.getMesh()),
@@ -339,16 +339,16 @@ void Output::doOutputAlways(Process const& process,
continue;
}
// mesh related output
- auto& mesh = *BaseLib::findElementOrError(
+ auto& non_bulk_mesh = *BaseLib::findElementOrError(
begin(_meshes), end(_meshes),
[&mesh_output_name](auto const& m) {
return m->getName() == mesh_output_name;
},
"Need mesh '" + mesh_output_name + "' for the output.");
- std::vector<MeshLib::Node*> const& nodes = mesh.getNodes();
+ std::vector<MeshLib::Node*> const& nodes = non_bulk_mesh.getNodes();
DBUG("Found {:d} nodes for output at mesh '{:s}'.", nodes.size(),
- mesh.getName());
+ non_bulk_mesh.getName());
std::vector<std::unique_ptr<NumLib::LocalToGlobalIndexMap>>
mesh_dof_tables;
@@ -357,7 +357,7 @@ void Output::doOutputAlways(Process const& process,
{
mesh_dof_tables.push_back(
process.getDOFTable(i).deriveBoundaryConstrainedMap(
- MeshLib::MeshSubset{mesh, nodes}));
+ MeshLib::MeshSubset{non_bulk_mesh, nodes}));
}
std::vector<NumLib::LocalToGlobalIndexMap const*>
mesh_dof_table_pointers;
@@ -369,18 +369,18 @@ void Output::doOutputAlways(Process const& process,
});
output_secondary_variable = false;
- addProcessDataToMesh(t, x, process_id, mesh, mesh_dof_table_pointers,
- process.getProcessVariables(process_id),
- process.getSecondaryVariables(),
- output_secondary_variable,
- process.getIntegrationPointWriter(mesh),
- _output_data_specification);
+ addProcessDataToMesh(
+ t, x, process_id, non_bulk_mesh, dof_tables,
+ mesh_dof_table_pointers, process.getProcessVariables(process_id),
+ process.getSecondaryVariables(), output_secondary_variable,
+ process.getIntegrationPointWriter(non_bulk_mesh),
+ _output_data_specification);
// TODO (TomFischer): add pvd support here. This can be done if the
// output is mesh related instead of process related. This would also
// allow for merging bulk mesh output and arbitrary mesh output.
- output_bulk_mesh(mesh);
+ output_bulk_mesh(non_bulk_mesh);
}
INFO("[time] Output of timestep {:d} took {:g} s.", timestep,
time_output.elapsed());
@@ -444,7 +444,7 @@ void Output::doOutputNonlinearIteration(Process const& process,
bool const output_secondary_variable = true;
addProcessDataToMesh(t, x, process_id, process.getMesh(), dof_tables,
- process.getProcessVariables(process_id),
+ dof_tables, process.getProcessVariables(process_id),
process.getSecondaryVariables(),
output_secondary_variable,
process.getIntegrationPointWriter(process.getMesh()),
diff --git a/ProcessLib/Output/ProcessOutput.cpp b/ProcessLib/Output/ProcessOutput.cpp
index 1a82f4e16ba..ae800fe77d8 100644
--- a/ProcessLib/Output/ProcessOutput.cpp
+++ b/ProcessLib/Output/ProcessOutput.cpp
@@ -19,6 +19,9 @@
#include "InfoLib/GitInfo.h"
#include "IntegrationPointWriter.h"
#include "MathLib/LinAlg/LinAlg.h"
+#ifdef USE_PETSC
+#include "MeshLib/NodePartitionedMesh.h"
+#endif
#include "MeshLib/IO/VtkIO/VtuInterface.h"
#include "MeshLib/IO/XDMF/XdmfHdfWriter.h"
#include "NumLib/DOF/LocalToGlobalIndexMap.h"
@@ -136,6 +139,8 @@ namespace ProcessLib
void addProcessDataToMesh(
const double t, std::vector<GlobalVector*> const& x, int const process_id,
MeshLib::Mesh& mesh,
+ [[maybe_unused]] std::vector<NumLib::LocalToGlobalIndexMap const*> const&
+ bulk_dof_table,
std::vector<NumLib::LocalToGlobalIndexMap const*> const& dof_table,
std::vector<std::reference_wrapper<ProcessVariable>> const&
process_variables,
@@ -207,6 +212,48 @@ void addProcessDataToMesh(
auto const mesh_id = mesh_subset.getMeshID();
for (auto const* node : mesh_subset.getNodes())
{
+#ifdef USE_PETSC
+ if (bulk_dof_table[process_id] != dof_table[process_id])
+ {
+ if (!mesh.getProperties().existsPropertyVector<std::size_t>(
+ "bulk_node_ids"))
+ {
+ OGS_FATAL(
+ "The required bulk node ids map does not exist in "
+ "the boundary mesh '{:s}' or has the wrong data "
+ "type (should be equivalent to C++ data type "
+ "std::size_t which is an unsigned integer of size "
+ "{:d} or UInt64 in vtk terminology).",
+ mesh.getName(), sizeof(std::size_t));
+ }
+ auto const bulk_node_id_map =
+ *mesh.getProperties().getPropertyVector<std::size_t>(
+ "bulk_node_ids");
+
+ if (static_cast<MeshLib::NodePartitionedMesh const&>(mesh)
+ .isGhostNode(node->getID()))
+ {
+ auto const bulk_node_id =
+ bulk_node_id_map[node->getID()];
+ // use bulk_dof_table to find information
+ std::size_t const bulk_mesh_id = 0;
+ MeshLib::Location const l(bulk_mesh_id,
+ MeshLib::MeshItemType::Node,
+ bulk_node_id);
+ auto const global_component_id =
+ global_component_offset + component_id;
+ auto const index =
+ bulk_dof_table[process_id]->getLocalIndex(
+ l, global_component_id,
+ x[process_id]->getRangeBegin(),
+ x[process_id]->getRangeEnd());
+
+ output_data[node->getID() * n_components +
+ component_id] = x_copy[index];
+ continue;
+ }
+ }
+#endif
MeshLib::Location const l(mesh_id, MeshLib::MeshItemType::Node,
node->getID());
diff --git a/ProcessLib/Output/ProcessOutput.h b/ProcessLib/Output/ProcessOutput.h
index 89b4cc631d1..028451aff6e 100644
--- a/ProcessLib/Output/ProcessOutput.h
+++ b/ProcessLib/Output/ProcessOutput.h
@@ -33,7 +33,8 @@ struct OutputDataSpecification final
void addProcessDataToMesh(
const double t, std::vector<GlobalVector*> const& x, int const process_id,
MeshLib::Mesh& mesh,
- std::vector<NumLib::LocalToGlobalIndexMap const*> const& dof_table,
+ std::vector<NumLib::LocalToGlobalIndexMap const*> const& bulk_dof_tables,
+ std::vector<NumLib::LocalToGlobalIndexMap const*> const& dof_tables,
std::vector<std::reference_wrapper<ProcessVariable>> const&
process_variables,
SecondaryVariableCollection const& secondary_variables,
--
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