diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.cpp b/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.cpp
index e9298be6f61764ed0136852331f3465d4cada1f7..7555f4b8f5cba0046de1d62e65b287a69ac31047 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.cpp
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.cpp
@@ -84,8 +84,8 @@ void NodeWiseMeshPartitioner::readMetisData(const std::string& file_name_base)
std::remove(fname_eparts.c_str());
}
-void NodeWiseMeshPartitioner
- ::partitionByMETIS(const bool is_mixed_high_order_linear_elems)
+void NodeWiseMeshPartitioner::partitionByMETIS(
+ const bool is_mixed_high_order_linear_elems)
{
std::vector<MeshLib::Node*> const& nodes = _mesh->getNodes();
for (std::size_t part_id = 0; part_id < _partitions.size(); part_id++)
@@ -186,8 +186,8 @@ void NodeWiseMeshPartitioner
renumberNodeIndices(is_mixed_high_order_linear_elems);
}
-void NodeWiseMeshPartitioner::renumberNodeIndices
- (const bool is_mixed_high_order_linear_elems)
+void NodeWiseMeshPartitioner::renumberNodeIndices(
+ const bool is_mixed_high_order_linear_elems)
{
std::size_t node_global_id_offset = 0;
// Renumber the global indices.
@@ -252,7 +252,7 @@ NodeWiseMeshPartitioner::IntegerType
NodeWiseMeshPartitioner::getNumberOfIntegerVariablesOfElements(
const std::vector<const MeshLib::Element*>& elements) const
{
- // Number of material ID, element type, and number of the nodes of
+ // Element ID, element type, and number of the nodes of
// an element of all elements in the current partition.
IntegerType nmb_element_idxs = 3 * elements.size();
for (const auto* elem : elements)
@@ -262,9 +262,10 @@ NodeWiseMeshPartitioner::getNumberOfIntegerVariablesOfElements(
return nmb_element_idxs;
}
-std::tuple< std::vector<NodeWiseMeshPartitioner::IntegerType>,
- std::vector<NodeWiseMeshPartitioner::IntegerType>>
-NodeWiseMeshPartitioner::writeConfigDataBinary(const std::string& file_name_base)
+std::tuple<std::vector<NodeWiseMeshPartitioner::IntegerType>,
+ std::vector<NodeWiseMeshPartitioner::IntegerType>>
+NodeWiseMeshPartitioner::writeConfigDataBinary(
+ const std::string& file_name_base)
{
const std::string fname = file_name_base + "_partitioned_msh_cfg"
+ std::to_string(_npartitions) + ".bin";
@@ -305,10 +306,10 @@ NodeWiseMeshPartitioner::writeConfigDataBinary(const std::string& file_name_base
// Update offsets
num_elem_integers[loop_id] =
partition.regular_elements.size() + config_data[8];
- // Offset the ending enrtry of the element integer variales of
+ // Offset the ending entry of the element integer variales of
// the non-ghost elements of this partition in the vector of elem_info.
config_data[11] += num_elem_integers[loop_id] * sizeof(IntegerType);
- // Offset the ending enrtry of the element integer variales of
+ // Offset the ending entry of the element integer variales of
// the ghost elements of this partition in the vector of elem_info.
num_g_elem_integers[loop_id] =
partition.ghost_elements.size() + config_data[9];
@@ -518,29 +519,6 @@ void NodeWiseMeshPartitioner::writeASCII(const std::string& file_name_base)
writeNodesASCII(file_name_base);
}
-void NodeWiseMeshPartitioner::resetGlobalNodeIndices()
-{
- for (std::size_t i = 0; i < _mesh->_nodes.size(); i++)
- {
- _mesh->_nodes[i]->setID(_nodes_global_ids[i]);
- }
- // sort
- std::sort(_mesh->_nodes.begin(), _mesh->_nodes.end(),
- [](const MeshLib::Node* a, const MeshLib::Node* b) {
- return a->getID() < b->getID();
- });
-}
-
-void NodeWiseMeshPartitioner::writeGlobalMeshVTU(
- const std::string& file_name_base)
-{
- resetGlobalNodeIndices();
- MeshLib::IO::VtuInterface writer(_mesh.get());
- const std::string npartitions_str = std::to_string(_npartitions);
- writer.writeToFile(file_name_base + "_node_id_renumbered_partitions_" +
- npartitions_str + ".vtu");
-}
-
void NodeWiseMeshPartitioner::getElementIntegerVariables(
const MeshLib::Element& elem,
const std::vector<IntegerType>& local_node_ids,
diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.h b/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.h
index c1505252263b5912773eafccc2afc8a78fcbe734..40f3fc3b1adee9db02003e607d30a32a23bec3c8 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.h
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.h
@@ -64,8 +64,6 @@ public:
/// interpolation
void partitionByMETIS(const bool is_mixed_high_order_linear_elems);
- void resetGlobalNodeIndices();
-
/// Read metis data
/// \param file_name_base The prefix of the file name.
void readMetisData(const std::string& file_name_base);
@@ -82,10 +80,6 @@ public:
/// \param file_name_base The prefix of the file name.
void writeBinary(const std::string& file_name_base);
- /// Write the global mesh into a VTU file
- /// \param file_name_base The prefix of the file name.
- void writeGlobalMeshVTU(const std::string& file_name_base);
-
private:
/// Number of partitions.
IntegerType _npartitions;
@@ -113,12 +107,11 @@ private:
/*!
Calculate the total number of integer variables of an element
- vector.
- Each element has three integer variables for material ID,
+ vector. Each element has three integer variables for element ID,
element type, number of nodes of the element. Therefore
the total number of the integers in an element vector is
3 * vector size + sum (number of nodes of each element)
- */
+ */
IntegerType getNumberOfIntegerVariablesOfElements(
const std::vector<const MeshLib::Element*>& elements) const;
diff --git a/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp b/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
index 3b6d8acfe6459d4c1ef86fa017cce095df143f65..69f5121ccd7f5ba80842836b0fca9edcc992e0f9 100644
--- a/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
+++ b/Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
@@ -134,9 +134,6 @@ int main(int argc, char* argv[])
INFO("Write the data of partitions into binary files ...");
mesh_partitioner.writeBinary(file_name_base);
}
-
- INFO("Write the mesh with renumbered node indices into VTU ...");
- mesh_partitioner.writeGlobalMeshVTU(file_name_base);
}
INFO("Total runtime: %g s.", run_timer.elapsed());
diff --git a/MeshLib/IO/MPI_IO/NodePartitionedMeshReader.h b/MeshLib/IO/MPI_IO/NodePartitionedMeshReader.h
index cf302e0fd76703933c28cb89027a98100e56c5c7..26e4a9f2488938d08d69b2813271c446b294499b 100644
--- a/MeshLib/IO/MPI_IO/NodePartitionedMeshReader.h
+++ b/MeshLib/IO/MPI_IO/NodePartitionedMeshReader.h
@@ -76,17 +76,24 @@ private:
/// A collection of integers that configure the partitioned mesh data.
struct PartitionedMeshInfo
{
- unsigned long nodes; ///< 0: Number of all nodes of a partition,
- unsigned long base_nodes; ///< 1: Number of nodes for linear elements of a parition,
- unsigned long regular_elements; ///< 2: Number of non-ghost elements of a partition,
- unsigned long ghost_elements; ///< 3: Number of ghost element of a partition,
- unsigned long active_base_nodes; ///< 4: Number of active nodes for linear element of a parition,
- unsigned long active_nodes; ///< 5: Number of all active nodes a parition,
- unsigned long global_base_nodes; ///< 6: Number of nodes for linear element of global mesh,
- unsigned long global_nodes; ///< 7: Number of all nodes of global mesh,
- unsigned long offset[5]; ///< 8~12: Offsets of positions of partitions in the data arrays
- /// (only 8 and 9 are used for ascii input)
- unsigned long extra_flag; ///< 13: Reserved for extra flag.
+ unsigned long nodes; ///< 0: Number of all nodes of a partition,
+ unsigned long base_nodes; ///< 1: Number of nodes for linear
+ ///elements of a parition,
+ unsigned long regular_elements; ///< 2: Number of non-ghost elements
+ ///of a partition,
+ unsigned long
+ ghost_elements; ///< 3: Number of ghost element of a partition,
+ unsigned long active_base_nodes; ///< 4: Number of active nodes for
+ /// linear element of a parition,
+ unsigned long
+ active_nodes; ///< 5: Number of all active nodes a parition,
+ unsigned long global_base_nodes; ///< 6: Number of nodes for linear
+ /// element of global mesh,
+ unsigned long global_nodes; ///< 7: Number of all nodes of global mesh,
+ unsigned long offset[5]; ///< 8~12: Offsets of positions of partitions
+ /// in the data arrays (only 8 and 9 are used
+ /// for ascii input)
+ unsigned long extra_flag; ///< 13: Reserved for extra flag.
std::size_t size() const { return 14; }
unsigned long* data() { return &nodes; }
diff --git a/MeshLib/Node.h b/MeshLib/Node.h
index cc62d741ccdd3b46b623d989af09bb9b217b24b0..e41a3aee1768a4d1e38b972db4b105581a041cc1 100644
--- a/MeshLib/Node.h
+++ b/MeshLib/Node.h
@@ -73,7 +73,7 @@ public:
return Node(_x[0]-v[0], _x[1]-v[1], _x[2]-v[2]);
}
-protected:
+private:
/// Update coordinates of a node.
/// This method automatically also updates the areas/volumes of all connected elements.
void updateCoordinates(double x, double y, double z);
diff --git a/MeshLib/NodePartitionedMesh.h b/MeshLib/NodePartitionedMesh.h
index f858ad3ac63691222e157309cde92c45f2054a51..0593b8c7d535201797e4c340575adb327e55cdf8 100644
--- a/MeshLib/NodePartitionedMesh.h
+++ b/MeshLib/NodePartitionedMesh.h
@@ -27,150 +27,143 @@ namespace MeshLib
/// A subdomain mesh.
class NodePartitionedMesh : public Mesh
{
- public:
- // Copy a global mesh for the case of the thread number is one,
- // i.e the gobal mesh is not partitioned.
- // \param mesh The gobal mesh
- explicit NodePartitionedMesh(const Mesh& mesh)
- : Mesh(mesh), _global_node_ids(mesh.getNumberOfNodes()),
- _n_global_base_nodes(mesh.getNumberOfBaseNodes()),
- _n_global_nodes(mesh.getNumberOfNodes()),
- _n_active_base_nodes(mesh.getNumberOfBaseNodes()),
- _n_active_nodes(mesh.getNumberOfNodes())
+public:
+ // Copy a global mesh for the case of the thread number is one,
+ // i.e the gobal mesh is not partitioned.
+ // \param mesh The gobal mesh
+ explicit NodePartitionedMesh(const Mesh& mesh)
+ : Mesh(mesh),
+ _global_node_ids(mesh.getNumberOfNodes()),
+ _n_global_base_nodes(mesh.getNumberOfBaseNodes()),
+ _n_global_nodes(mesh.getNumberOfNodes()),
+ _n_active_base_nodes(mesh.getNumberOfBaseNodes()),
+ _n_active_nodes(mesh.getNumberOfNodes())
+ {
+ const auto& mesh_nodes = mesh.getNodes();
+ for (std::size_t i = 0; i < _nodes.size(); i++)
{
- const auto& mesh_nodes = mesh.getNodes();
- for (std::size_t i = 0; i < _nodes.size(); i++)
+ _global_node_ids[i] = _nodes[i]->getID();
+
+ // TODO To add copying of the connected nodes (and elements)
+ // in the copy constructor of class Node in order to
+ // drop the following lines.
+ auto node = _nodes[i];
+ // Copy constructor of Mesh does not copy the connected
+ // nodes to node.
+ if (node->_connected_nodes.size() == 0)
{
- _global_node_ids[i] = _nodes[i]->getID();
-
- // TODO To add copying of the connected nodes (and elements)
- // in the copy constructor of class Node in order to
- // drop the following lines.
- auto node = _nodes[i];
- // Copy constructor of Mesh does not copy the connected
- // nodes to node.
- if (node->_connected_nodes.size() == 0)
- {
- std::copy(mesh_nodes[i]->_connected_nodes.begin(),
- mesh_nodes[i]->_connected_nodes.end(),
- std::back_inserter(node->_connected_nodes));
- }
+ std::copy(mesh_nodes[i]->_connected_nodes.begin(),
+ mesh_nodes[i]->_connected_nodes.end(),
+ std::back_inserter(node->_connected_nodes));
}
}
-
- /*!
- \brief Constructor
- \param name Name assigned to the mesh.
- \param nodes Vector for nodes, which storage looks like:
- ||--active base nodes--|--ghost base nodes--|
- --active extra nodes--|--ghost extra nodes--||
- (extra nodes: nodes for high order interpolations)
- \param glb_node_ids Global IDs of nodes of a partition.
- \param elements Vector for elements. Ghost elements are stored
- after regular (non-ghost) elements.
- \param properties Mesh property.
- \param n_global_base_nodes Number of the base nodes of the global mesh.
- \param n_global_nodes Number of all nodes of the global mesh.
- \param n_base_nodes Number of the base nodes.
- \param n_active_base_nodes Number of the active base nodes.
- \param n_active_nodes Number of all active nodes.
- */
- NodePartitionedMesh(const std::string &name,
- const std::vector<Node*> &nodes,
- const std::vector<std::size_t> &glb_node_ids,
- const std::vector<Element*> &elements,
- Properties properties,
- const std::size_t n_global_base_nodes,
- const std::size_t n_global_nodes,
- const std::size_t n_base_nodes,
- const std::size_t n_active_base_nodes,
- const std::size_t n_active_nodes)
- : Mesh(name, nodes, elements, properties, n_base_nodes),
- _global_node_ids(glb_node_ids),
- _n_global_base_nodes(n_global_base_nodes),
- _n_global_nodes(n_global_nodes),
- _n_active_base_nodes(n_active_base_nodes),
- _n_active_nodes(n_active_nodes)
- {
- }
-
- /// Get the number of nodes of the global mesh for linear elements.
- std::size_t getNumberOfGlobalBaseNodes() const
- {
- return _n_global_base_nodes;
- }
-
- /// Get the number of all nodes of the global mesh.
- std::size_t getNumberOfGlobalNodes() const
- {
- return _n_global_nodes;
- }
-
- /// Get the global node ID of a node with its local ID.
- std::size_t getGlobalNodeID(const std::size_t node_id) const
- {
- return _global_node_ids[node_id];
- }
-
- /// Get the number of the active nodes of the partition for linear elements.
- std::size_t getNumberOfActiveBaseNodes() const
- {
- return _n_active_base_nodes;
- }
-
- /// Get the number of all active nodes of the partition.
- std::size_t getNumberOfActiveNodes() const
- {
- return _n_active_nodes;
- }
-
- /// Check whether a node with ID of node_id is a ghost node
- bool isGhostNode(const std::size_t node_id) const
- {
- if(node_id < _n_active_base_nodes)
- return false;
- else if(node_id >= _n_base_nodes && node_id < getLargestActiveNodeID() )
- return false;
- else
- return true;
- }
-
- /// Get the largest ID of active nodes for higher order elements in a partition.
- std::size_t getLargestActiveNodeID() const
- {
- return _n_base_nodes + _n_active_nodes - _n_active_base_nodes;
- }
-
- // TODO I guess that is a simplified version of computeSparsityPattern()
- /// Get the maximum number of connected nodes to node.
- std::size_t getMaximumNConnectedNodesToNode() const
- {
- std::vector<Node *>::const_iterator it_max_ncn = std::max_element(
- _nodes.cbegin(), _nodes.cend(),
- [](Node const *const node_a, Node const *const node_b)
- {
- return (node_a->getConnectedNodes().size() <
- node_b->getConnectedNodes().size());
- });
- // Return the number of connected nodes +1 for the node itself.
- return (*it_max_ncn)->getConnectedNodes().size() + 1;
- }
-
- private:
- /// Global IDs of nodes of a partition
- std::vector<std::size_t> _global_node_ids;
-
- /// Number of the nodes of the global mesh linear interpolations.
- std::size_t _n_global_base_nodes;
-
- /// Number of all nodes of the global mesh.
- std::size_t _n_global_nodes;
-
- /// Number of the active nodes for linear interpolations
- std::size_t _n_active_base_nodes;
-
- /// Number of the all active nodes.
- std::size_t _n_active_nodes;
+ }
+
+ /*!
+ \brief Constructor
+ \param name Name assigned to the mesh.
+ \param nodes Vector for nodes, which storage looks like:
+ ||--active base nodes--|--ghost base nodes--|
+ --active extra nodes--|--ghost extra nodes--||
+ (extra nodes: nodes for high order interpolations)
+ \param glb_node_ids Global IDs of nodes of a partition.
+ \param elements Vector for elements. Ghost elements are stored
+ after regular (non-ghost) elements.
+ \param properties Mesh property.
+ \param n_global_base_nodes Number of the base nodes of the global mesh.
+ \param n_global_nodes Number of all nodes of the global mesh.
+ \param n_base_nodes Number of the base nodes.
+ \param n_active_base_nodes Number of the active base nodes.
+ \param n_active_nodes Number of all active nodes.
+ */
+ NodePartitionedMesh(const std::string& name,
+ const std::vector<Node*>& nodes,
+ const std::vector<std::size_t>& glb_node_ids,
+ const std::vector<Element*>& elements,
+ Properties properties,
+ const std::size_t n_global_base_nodes,
+ const std::size_t n_global_nodes,
+ const std::size_t n_base_nodes,
+ const std::size_t n_active_base_nodes,
+ const std::size_t n_active_nodes)
+ : Mesh(name, nodes, elements, properties, n_base_nodes),
+ _global_node_ids(glb_node_ids),
+ _n_global_base_nodes(n_global_base_nodes),
+ _n_global_nodes(n_global_nodes),
+ _n_active_base_nodes(n_active_base_nodes),
+ _n_active_nodes(n_active_nodes)
+ {
+ }
+
+ /// Get the number of nodes of the global mesh for linear elements.
+ std::size_t getNumberOfGlobalBaseNodes() const
+ {
+ return _n_global_base_nodes;
+ }
+
+ /// Get the number of all nodes of the global mesh.
+ std::size_t getNumberOfGlobalNodes() const { return _n_global_nodes; }
+ /// Get the global node ID of a node with its local ID.
+ std::size_t getGlobalNodeID(const std::size_t node_id) const
+ {
+ return _global_node_ids[node_id];
+ }
+
+ /// Get the number of the active nodes of the partition for linear elements.
+ std::size_t getNumberOfActiveBaseNodes() const
+ {
+ return _n_active_base_nodes;
+ }
+
+ /// Get the number of all active nodes of the partition.
+ std::size_t getNumberOfActiveNodes() const { return _n_active_nodes; }
+ /// Check whether a node with ID of node_id is a ghost node
+ bool isGhostNode(const std::size_t node_id) const
+ {
+ if (node_id < _n_active_base_nodes)
+ return false;
+ else if (node_id >= _n_base_nodes && node_id < getLargestActiveNodeID())
+ return false;
+ else
+ return true;
+ }
+
+ /// Get the largest ID of active nodes for higher order elements in a
+ /// partition.
+ std::size_t getLargestActiveNodeID() const
+ {
+ return _n_base_nodes + _n_active_nodes - _n_active_base_nodes;
+ }
+
+ // TODO I guess that is a simplified version of computeSparsityPattern()
+ /// Get the maximum number of connected nodes to node.
+ std::size_t getMaximumNConnectedNodesToNode() const
+ {
+ std::vector<Node*>::const_iterator it_max_ncn = std::max_element(
+ _nodes.cbegin(), _nodes.cend(),
+ [](Node const* const node_a, Node const* const node_b) {
+ return (node_a->getConnectedNodes().size() <
+ node_b->getConnectedNodes().size());
+ });
+ // Return the number of connected nodes +1 for the node itself.
+ return (*it_max_ncn)->getConnectedNodes().size() + 1;
+ }
+
+private:
+ /// Global IDs of nodes of a partition
+ std::vector<std::size_t> _global_node_ids;
+
+ /// Number of the nodes of the global mesh linear interpolations.
+ std::size_t _n_global_base_nodes;
+
+ /// Number of all nodes of the global mesh.
+ std::size_t _n_global_nodes;
+
+ /// Number of the active nodes for linear interpolations
+ std::size_t _n_active_base_nodes;
+
+ /// Number of the all active nodes.
+ std::size_t _n_active_nodes;
};
} // namespace MeshLib
diff --git a/MeshLib/PropertyVector.h b/MeshLib/PropertyVector.h
index 8117734547413bee1f1ba0bf78fde533e878f534..37b285ccf9d180a1648feb82fdbb59c03594b284 100644
--- a/MeshLib/PropertyVector.h
+++ b/MeshLib/PropertyVector.h
@@ -22,9 +22,6 @@
namespace MeshLib
{
-
-//template <typename T> class PropertyVector;
-
class PropertyVectorBase
{
public:
@@ -86,10 +83,11 @@ public:
component);
}
- PropertyVectorBase* clone(std::vector<std::size_t> const& exclude_positions) const
+ PropertyVectorBase* clone(
+ std::vector<std::size_t> const& exclude_positions) const
{
- PropertyVector<PROP_VAL_TYPE> *t(new PropertyVector<PROP_VAL_TYPE>(_property_name,
- _mesh_item_type, _n_components));
+ PropertyVector<PROP_VAL_TYPE>* t(new PropertyVector<PROP_VAL_TYPE>(
+ _property_name, _mesh_item_type, _n_components));
BaseLib::excludeObjectCopy(*this, exclude_positions, *t);
return t;
}
@@ -220,7 +218,7 @@ public:
assert(component < _n_components);
assert(tuple_index < getNumberOfTuples());
const double* p = this->operator[](tuple_index);
- if (p==nullptr)
+ if (p == nullptr)
OGS_FATAL("No data found in the property vector %s "
"for the tuple index %d and component %d",
getPropertyName().c_str(), tuple_index, component);
@@ -235,7 +233,8 @@ public:
std::copy(this->cbegin(), this->cend(),
std::ostream_iterator<std::size_t>(os, " "));
os << "\n\tvalues (" << _values.size() << "):\n";
- for (std::size_t k(0); k<_values.size(); k++) {
+ for (std::size_t k(0); k < _values.size(); k++)
+ {
os << "val: " << *(_values[k]) << ", address: " << _values[k] << "\n";
}
return os;
diff --git a/ProcessLib/LiquidFlow/LiquidFlowMaterialProperties.cpp b/ProcessLib/LiquidFlow/LiquidFlowMaterialProperties.cpp
index 2f99c1360cff4e955f7a0a1470d7859660a92501..be8dabcb684f031ae37efb534c4f1badef7297ed 100644
--- a/ProcessLib/LiquidFlow/LiquidFlowMaterialProperties.cpp
+++ b/ProcessLib/LiquidFlow/LiquidFlowMaterialProperties.cpp
@@ -24,7 +24,6 @@
#include "MaterialLib/Fluid/FluidProperty.h"
#include "MaterialLib/PorousMedium/Porosity/Porosity.h"
#include "MaterialLib/PorousMedium/Storage/Storage.h"
-#include "MaterialLib/Fluid/FluidProperties/CreateFluidProperties.h"
#include "MaterialLib/Fluid/FluidPropertyHeaders.h"
#include "MaterialLib/PorousMedium/PorousPropertyHeaders.h"